From nek5000-users at lists.mcs.anl.gov Wed Sep 4 08:33:51 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Sep 2013 09:33:51 -0400 Subject: [Nek5000-users] Problem reading binary .fld files into postnek Message-ID: Hi Neks, I am having some issues importing my binary-type data into postnek. When the files are imported into postnek, many of the elements are missing and this is part of the message that appears in the terminal: -Adobe-Helvetica-Medium-R-Normal--12-120-75-75-P-67-ISO8859-1 NEKTON Version 2.6 I/O Error: No String Terminator sent to PRS Enter Session Name (Default= g40cond_as I/O Error: No String Terminator sent to PRS Beginning Session g40cond_as renaming SESSION.NAME SESSION.NAME~ Session name:"g40cond_as " cp: /Users/chris/.nekdefaults: No such file or directory renaming g40cond_as.plt01 g40cond_as.plt01~ LTRUNC: string: 80 LTRUNC: string: 28 Wed Sep 4 09:30:51 EDT 2013 I/O Error: No String Terminator sent to PRS Reading geometry from XYZ Min,Max: -40.0000 40.0000 -40.0000 40.0000 0.00000 1.00000 1 3017 1 TRYING TO READ BC 7 3072 2 TRYING TO READ BC 7 3072 3 TRYING TO READ BC 7 3072 4 TRYING TO READ BC 7 3072 5 TRYING TO READ BC Error reading options in .REA file this is iffmat: F 4.0000000 g40cond_as g40cond_as.fld01 The same data can be read correctly in Visit, however. Any ideas? Additionally, if this problem cannot be overcome, is there a way to take profile points using Visit or Matlab? Thank you for your help, Chris -- Christopher O. Mehrvarzi Paul Research Group Virginia Tech - Mechanical Engineering chrisom3 at vt.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Sep 4 08:49:03 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Sep 2013 08:49:03 -0500 (CDT) Subject: [Nek5000-users] Problem reading binary .fld files into postnek In-Reply-To: References: Message-ID: Chris, What type of .rea file do you have ? (Do you have .re2, or just standard .rea?) Also, take a look at p66 and p67 in your .rea file -- they should either be 4 or 6, depending on whether your file extension is .fld or .f00000 My guess is that fixing those values should resolve the issue. Please let me know if this works. Best, Paul On Wed, 4 Sep 2013, nek5000-users at lists.mcs.anl.gov wrote: > Hi Neks, > > I am having some issues importing my binary-type data into postnek. When > the files are imported into postnek, many of the elements are missing and > this is part of the message that appears in the terminal: > > > -Adobe-Helvetica-Medium-R-Normal--12-120-75-75-P-67-ISO8859-1 > NEKTON Version 2.6 > > I/O Error: No String Terminator sent to PRS > Enter Session Name (Default= g40cond_as > > I/O Error: No String Terminator sent to PRS > Beginning Session g40cond_as > > renaming SESSION.NAME SESSION.NAME~ > Session name:"g40cond_as > " > cp: /Users/chris/.nekdefaults: No such file or directory > renaming g40cond_as.plt01 g40cond_as.plt01~ > > LTRUNC: string: 80 > > LTRUNC: string: 28 > Wed Sep 4 09:30:51 EDT 2013 > I/O Error: No String Terminator sent to PRS > Reading geometry from > XYZ Min,Max: > -40.0000 40.0000 > -40.0000 40.0000 > 0.00000 1.00000 > 1 3017 1 TRYING TO READ BC > 7 3072 2 TRYING TO READ BC > 7 3072 3 TRYING TO READ BC > 7 3072 4 TRYING TO READ BC > 7 3072 5 TRYING TO READ BC > Error reading options in .REA file > > this is iffmat: F 4.0000000 > g40cond_as > > g40cond_as.fld01 > > > > The same data can be read correctly in Visit, however. Any ideas? > > Additionally, if this problem cannot be overcome, is there a way to take > profile points using Visit or Matlab? > > Thank you for your help, > > Chris > > > -- > Christopher O. Mehrvarzi > Paul Research Group > Virginia Tech - Mechanical Engineering > chrisom3 at vt.edu > From nek5000-users at lists.mcs.anl.gov Wed Sep 4 10:30:44 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Sep 2013 17:30:44 +0200 Subject: [Nek5000-users] 3D Problem Visual Message-ID: Dear All, I have the following problem when visualizing 3D results (see link to picture below); http://s17.postimg.org/zcdn91qkv/Capture.png There seems to be some overlapping problem or connection problem between sections of the geometry. I have created the 2D face geometry with prex and then extruded to 3D using n2to3. Could it be I am doing something wrong in prex? I first created 3 different elements; two cuboids and the middle section that contains the bump. Then I refined the mesh in each of the three elements using the multi-split. Thank you in advance, JP -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Sep 4 10:40:06 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Sep 2013 17:40:06 +0200 Subject: [Nek5000-users] 3D Problem Visual Message-ID: Dear All, This is another example of the same problem but with a much finer mesh: http://s14.postimg.org/5b5rymzht/Capture2.png (Sorry for not posting in one message) Thanks, JP -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Sep 4 11:11:06 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Sep 2013 11:11:06 -0500 (CDT) Subject: [Nek5000-users] 3D Problem Visual In-Reply-To: Message-ID: JP, You could try the following in usrdat2() call fix_geom ... This will try to glue geometry together that is close but not perfect. Aside from the visual annoyance, do the results otherwise look correct? Best, Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: "nek5000-users" Sent: Wednesday, September 4, 2013 10:40:06 AM Subject: Re: [Nek5000-users] 3D Problem Visual Dear All, This is another example of the same problem but with a much finer mesh: http://s14.postimg.org/5b5rymzht/Capture2.png (Sorry for not posting in one message) Thanks, JP _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Wed Sep 4 13:46:00 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Sep 2013 14:46:00 -0400 Subject: [Nek5000-users] Problem reading binary .fld files into postnek In-Reply-To: References: Message-ID: Hi Paul, Thank you for your suggestions. I am using a standard .rea file and already had the flags at p66 and p67 set to 4 (the extension of my data is .fld) but the problem still occurs. I tried setting the flags to 6 anyways but still encountered the same problem. Chris On Wed, Sep 4, 2013 at 9:33 AM, Christopher Mehrvarzi wrote: > Hi Neks, > > I am having some issues importing my binary-type data into postnek. When > the files are imported into postnek, many of the elements are missing and > this is part of the message that appears in the terminal: > > > -Adobe-Helvetica-Medium-R-Normal--12-120-75-75-P-67-ISO8859-1 > NEKTON Version 2.6 > > I/O Error: No String Terminator sent to PRS > Enter Session Name (Default= g40cond_as > > I/O Error: No String Terminator sent to PRS > Beginning Session g40cond_as > > renaming SESSION.NAME SESSION.NAME~ > Session name:"g40cond_as > " > cp: /Users/chris/.nekdefaults: No such file or directory > renaming g40cond_as.plt01 g40cond_as.plt01~ > > LTRUNC: string: 80 > > LTRUNC: string: 28 > Wed Sep 4 09:30:51 EDT 2013 > I/O Error: No String Terminator sent to PRS > Reading geometry from > XYZ Min,Max: > -40.0000 40.0000 > -40.0000 40.0000 > 0.00000 1.00000 > 1 3017 1 TRYING TO READ BC > 7 3072 2 TRYING TO READ BC > 7 3072 3 TRYING TO READ BC > 7 3072 4 TRYING TO READ BC > 7 3072 5 TRYING TO READ BC > Error reading options in .REA file > > this is iffmat: F 4.0000000 > g40cond_as > > g40cond_as.fld01 > > > > The same data can be read correctly in Visit, however. Any ideas? > > Additionally, if this problem cannot be overcome, is there a way to take > profile points using Visit or Matlab? > > Thank you for your help, > > Chris > > > -- > Christopher O. Mehrvarzi > Paul Research Group > Virginia Tech - Mechanical Engineering > chrisom3 at vt.edu > > -- Christopher O. Mehrvarzi Paul Research Group Virginia Tech - Mechanical Engineering chrisom3 at vt.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Sep 4 14:59:21 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Sep 2013 14:59:21 -0500 (CDT) Subject: [Nek5000-users] Problem reading binary .fld files into postnek In-Reply-To: Message-ID: Hi Chris, Is your file format .fld or f0000 ? Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Wednesday, September 4, 2013 1:46:00 PM Subject: Re: [Nek5000-users] Problem reading binary .fld files into postnek Hi Paul, Thank you for your suggestions. I am using a standard .rea file and already had the flags at p66 and p67 set to 4 (the extension of my data is .fld) but the problem still occurs. I tried setting the flags to 6 anyways but still encountered the same problem. Chris On Wed, Sep 4, 2013 at 9:33 AM, Christopher Mehrvarzi < chrisom3 at vt.edu > wrote: Hi Neks, I am having some issues importing my binary-type data into postnek. When the files are imported into postnek, many of the elements are missing and this is part of the message that appears in the terminal: -Adobe-Helvetica-Medium-R-Normal--12-120-75-75-P-67-ISO8859-1 NEKTON Version 2.6 I/O Error: No String Terminator sent to PRS Enter Session Name (Default= g40cond_as I/O Error: No String Terminator sent to PRS Beginning Session g40cond_as renaming SESSION.NAME SESSION.NAME ~ Session name:"g40cond_as " cp: /Users/chris/.nekdefaults: No such file or directory renaming g40cond_as.plt01 g40cond_as.plt01~ LTRUNC: string: 80 LTRUNC: string: 28 Wed Sep 4 09:30:51 EDT 2013 I/O Error: No String Terminator sent to PRS Reading geometry from XYZ Min,Max: -40.0000 40.0000 -40.0000 40.0000 0.00000 1.00000 1 3017 1 TRYING TO READ BC 7 3072 2 TRYING TO READ BC 7 3072 3 TRYING TO READ BC 7 3072 4 TRYING TO READ BC 7 3072 5 TRYING TO READ BC Error reading options in .REA file this is iffmat: F 4.0000000 g40cond_as g40cond_as.fld01 The same data can be read correctly in Visit, however. Any ideas? Additionally, if this problem cannot be overcome, is there a way to take profile points using Visit or Matlab? Thank you for your help, Chris -- Christopher O. Mehrvarzi Paul Research Group Virginia Tech - Mechanical Engineering chrisom3 at vt.edu -- Christopher O. Mehrvarzi Paul Research Group Virginia Tech - Mechanical Engineering chrisom3 at vt.edu _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Wed Sep 4 15:43:35 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Sep 2013 15:43:35 -0500 Subject: [Nek5000-users] Problem reading binary .fld files into postnek In-Reply-To: References: Message-ID: Hi Chris, Are you using the current version of postnek? Katie On Wed, Sep 4, 2013 at 1:46 PM, wrote: > Hi Paul, > > Thank you for your suggestions. I am using a standard .rea file and > already had the flags at p66 and p67 set to 4 (the extension of my data > is .fld) but the problem still occurs. I tried setting the flags to 6 > anyways but still encountered the same problem. > > Chris > > > On Wed, Sep 4, 2013 at 9:33 AM, Christopher Mehrvarzi wrote: > >> Hi Neks, >> >> I am having some issues importing my binary-type data into postnek. When >> the files are imported into postnek, many of the elements are missing and >> this is part of the message that appears in the terminal: >> >> >> -Adobe-Helvetica-Medium-R-Normal--12-120-75-75-P-67-ISO8859-1 >> NEKTON Version 2.6 >> >> I/O Error: No String Terminator sent to PRS >> Enter Session Name (Default= g40cond_as >> >> I/O Error: No String Terminator sent to PRS >> Beginning Session g40cond_as >> >> renaming SESSION.NAME SESSION.NAME~ >> Session name:"g40cond_as >> " >> cp: /Users/chris/.nekdefaults: No such file or directory >> renaming g40cond_as.plt01 g40cond_as.plt01~ >> >> LTRUNC: string: 80 >> >> LTRUNC: string: 28 >> Wed Sep 4 09:30:51 EDT 2013 >> I/O Error: No String Terminator sent to PRS >> Reading geometry from >> XYZ Min,Max: >> -40.0000 40.0000 >> -40.0000 40.0000 >> 0.00000 1.00000 >> 1 3017 1 TRYING TO READ BC >> 7 3072 2 TRYING TO READ BC >> 7 3072 3 TRYING TO READ BC >> 7 3072 4 TRYING TO READ BC >> 7 3072 5 TRYING TO READ BC >> Error reading options in .REA file >> >> this is iffmat: F 4.0000000 >> g40cond_as >> >> g40cond_as.fld01 >> >> >> >> The same data can be read correctly in Visit, however. Any ideas? >> >> Additionally, if this problem cannot be overcome, is there a way to take >> profile points using Visit or Matlab? >> >> Thank you for your help, >> >> Chris >> >> >> -- >> Christopher O. Mehrvarzi >> Paul Research Group >> Virginia Tech - Mechanical Engineering >> chrisom3 at vt.edu >> >> > > > -- > Christopher O. Mehrvarzi > Paul Research Group > Virginia Tech - Mechanical Engineering > chrisom3 at vt.edu > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Sep 5 07:49:01 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 05 Sep 2013 14:49:01 +0200 Subject: [Nek5000-users] Optimal response for nek5000 Message-ID: Dear neks I'm going to implement optimal response to forcing in nekton and I have question related to pressure solver. During calculations I have to continuously switch between time dependent N-S and Stokes problem. I was going to do something similar to prsolvv. However, in nek_init the choice of pressure solver depends on IFTRAN suggesting different solver for Stokes problem, but prslovv seem to be called without reinitialisation of pressure solver. So can I use the same pressure solver (say itr) for both full N-S and Stokes? Regards Adam From nek5000-users at lists.mcs.anl.gov Thu Sep 5 08:46:12 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 5 Sep 2013 08:46:12 -0500 (CDT) Subject: [Nek5000-users] Optimal response for nek5000 In-Reply-To: Message-ID: Adam, Just to clarify, are you switching between time-dependent NS and time-dependent Stokes. Or, are you switching between time-dependent NS and steady Stokes ? Also, are you using PnPn or PnPn-2 ? Thanks, Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Thursday, September 5, 2013 7:49:01 AM Subject: [Nek5000-users] Optimal response for nek5000 Dear neks I'm going to implement optimal response to forcing in nekton and I have question related to pressure solver. During calculations I have to continuously switch between time dependent N-S and Stokes problem. I was going to do something similar to prsolvv. However, in nek_init the choice of pressure solver depends on IFTRAN suggesting different solver for Stokes problem, but prslovv seem to be called without reinitialisation of pressure solver. So can I use the same pressure solver (say itr) for both full N-S and Stokes? Regards Adam _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Thu Sep 5 09:11:19 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 05 Sep 2013 16:11:19 +0200 Subject: [Nek5000-users] Optimal response for nek5000 In-Reply-To: References: Message-ID: Dear Paul I switch between time-dependent NS and time-dependent Stokes (both for Euler time-stepping). I missed the fact that prsolvv gives steady state solution. I guess it will be PnPn-2, but not sure. Is there a crucial difference between PnPn and PnPn-2 when it comes to switching between NS and Stokes? regards Adam On 05/09/13 15:46, nek5000-users at lists.mcs.anl.gov wrote: > Adam, > > Just to clarify, > > are you switching between time-dependent NS and time-dependent Stokes. > > Or, are you switching between time-dependent NS and steady Stokes ? > > Also, are you using PnPn or PnPn-2 ? > > Thanks, > > Paul > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Sent: Thursday, September 5, 2013 7:49:01 AM > Subject: [Nek5000-users] Optimal response for nek5000 > > Dear neks > > I'm going to implement optimal response to forcing in nekton and I have > question related to pressure solver. During calculations I have to > continuously switch between time dependent N-S and Stokes problem. I was > going to do something similar to prsolvv. However, in nek_init the > choice of pressure solver depends on IFTRAN suggesting different solver > for Stokes problem, but prslovv seem to be called without > reinitialisation of pressure solver. So can I use the same pressure > solver (say itr) for both full N-S and Stokes? > Regards > Adam > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Thu Sep 5 09:33:57 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 5 Sep 2013 09:33:57 -0500 (CDT) Subject: [Nek5000-users] Optimal response for nek5000 In-Reply-To: Message-ID: Dear Adam, I first need to understand if you are solving .steady Stokes or .unsteady Stokes They differ by what is on the diagonal of the Stokes operator. For steady Stokes - A -D' -D 0 for unsteady Stokes we have H -D' -D 0 where H = 1/dt*B + A The conditioning of the systems is quite different and hence the solution strategy is also different. For steady Stokes, I can confirm that PnPn-2 works well --- I'm less certain of PnPn, which is generally designed as a high Reynolds number solver (but it also works fine at low Re, I'm just not certain of Re=0 for PnPn). Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Thursday, September 5, 2013 9:11:19 AM Subject: Re: [Nek5000-users] Optimal response for nek5000 Dear Paul I switch between time-dependent NS and time-dependent Stokes (both for Euler time-stepping). I missed the fact that prsolvv gives steady state solution. I guess it will be PnPn-2, but not sure. Is there a crucial difference between PnPn and PnPn-2 when it comes to switching between NS and Stokes? regards Adam On 05/09/13 15:46, nek5000-users at lists.mcs.anl.gov wrote: > Adam, > > Just to clarify, > > are you switching between time-dependent NS and time-dependent Stokes. > > Or, are you switching between time-dependent NS and steady Stokes ? > > Also, are you using PnPn or PnPn-2 ? > > Thanks, > > Paul > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Sent: Thursday, September 5, 2013 7:49:01 AM > Subject: [Nek5000-users] Optimal response for nek5000 > > Dear neks > > I'm going to implement optimal response to forcing in nekton and I have > question related to pressure solver. During calculations I have to > continuously switch between time dependent N-S and Stokes problem. I was > going to do something similar to prsolvv. However, in nek_init the > choice of pressure solver depends on IFTRAN suggesting different solver > for Stokes problem, but prslovv seem to be called without > reinitialisation of pressure solver. So can I use the same pressure > solver (say itr) for both full N-S and Stokes? > Regards > Adam > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Thu Sep 5 09:46:18 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 5 Sep 2013 09:46:18 -0500 (CDT) Subject: [Nek5000-users] Optimal response for nek5000 In-Reply-To: Message-ID: PS --- sorry, I mis-read this before. time-dependent NS and time-dependent Stokes: .PnPn or PnPn-2 are equally fine .There is no need to switch to the steady Stokes solver So, I would just use a call to incomprn() Best, Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Thursday, September 5, 2013 9:11:19 AM Subject: Re: [Nek5000-users] Optimal response for nek5000 Dear Paul I switch between time-dependent NS and time-dependent Stokes (both for Euler time-stepping). I missed the fact that prsolvv gives steady state solution. I guess it will be PnPn-2, but not sure. Is there a crucial difference between PnPn and PnPn-2 when it comes to switching between NS and Stokes? regards Adam On 05/09/13 15:46, nek5000-users at lists.mcs.anl.gov wrote: > Adam, > > Just to clarify, > > are you switching between time-dependent NS and time-dependent Stokes. > > Or, are you switching between time-dependent NS and steady Stokes ? > > Also, are you using PnPn or PnPn-2 ? > > Thanks, > > Paul > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Sent: Thursday, September 5, 2013 7:49:01 AM > Subject: [Nek5000-users] Optimal response for nek5000 > > Dear neks > > I'm going to implement optimal response to forcing in nekton and I have > question related to pressure solver. During calculations I have to > continuously switch between time dependent N-S and Stokes problem. I was > going to do something similar to prsolvv. However, in nek_init the > choice of pressure solver depends on IFTRAN suggesting different solver > for Stokes problem, but prslovv seem to be called without > reinitialisation of pressure solver. So can I use the same pressure > solver (say itr) for both full N-S and Stokes? > Regards > Adam > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Sep 6 04:13:19 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 6 Sep 2013 11:13:19 +0200 Subject: [Nek5000-users] 3D Problem Visual Message-ID: Hi Paul, Thank you, calling fix_geom in usrdat2() solved the problem. The results seem to be good even without the fix_geom, the problem with the geometry doesn't seem to interfere with the flow... but due to the problems with visualisation it is difficult to be 100% certain. Thanks again, JP -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Sep 9 04:17:04 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 9 Sep 2013 11:17:04 +0200 Subject: [Nek5000-users] 3D Problem Visual Message-ID: Hi Paul and all, Unfortunately, even with fix_geom in usrdat2(), some geometry problems (strange column like geometry problems at the back of the channel) are still occurring when I tried a different mesh. See below: http://s22.postimg.org/5hu13y1gx/Screen_Shot_2013_09_09_at_11_06_52.png The results seem correct though. The geometry problem does not interfere with the flow. Thank you, JP -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Sep 9 13:11:51 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 9 Sep 2013 14:11:51 -0400 Subject: [Nek5000-users] Problem reading binary .fld files into postnek In-Reply-To: References: Message-ID: Hi Neks, I apologize for the delayed response. Thank you for your suggestions. Paul -- my files are in .fld format. Kate -- I was using an older version of postnek. I compiled the latest version on my computer and tried again, but I'm still running into problems. Thank you for your time, Chris On Wed, Sep 4, 2013 at 2:46 PM, Christopher Mehrvarzi wrote: > Hi Paul, > > Thank you for your suggestions. I am using a standard .rea file and > already had the flags at p66 and p67 set to 4 (the extension of my data > is .fld) but the problem still occurs. I tried setting the flags to 6 > anyways but still encountered the same problem. > > Chris > > > On Wed, Sep 4, 2013 at 9:33 AM, Christopher Mehrvarzi wrote: > >> Hi Neks, >> >> I am having some issues importing my binary-type data into postnek. When >> the files are imported into postnek, many of the elements are missing and >> this is part of the message that appears in the terminal: >> >> >> -Adobe-Helvetica-Medium-R-Normal--12-120-75-75-P-67-ISO8859-1 >> NEKTON Version 2.6 >> >> I/O Error: No String Terminator sent to PRS >> Enter Session Name (Default= g40cond_as >> >> I/O Error: No String Terminator sent to PRS >> Beginning Session g40cond_as >> >> renaming SESSION.NAME SESSION.NAME~ >> Session name:"g40cond_as >> " >> cp: /Users/chris/.nekdefaults: No such file or directory >> renaming g40cond_as.plt01 g40cond_as.plt01~ >> >> LTRUNC: string: 80 >> >> LTRUNC: string: 28 >> Wed Sep 4 09:30:51 EDT 2013 >> I/O Error: No String Terminator sent to PRS >> Reading geometry from >> XYZ Min,Max: >> -40.0000 40.0000 >> -40.0000 40.0000 >> 0.00000 1.00000 >> 1 3017 1 TRYING TO READ BC >> 7 3072 2 TRYING TO READ BC >> 7 3072 3 TRYING TO READ BC >> 7 3072 4 TRYING TO READ BC >> 7 3072 5 TRYING TO READ BC >> Error reading options in .REA file >> >> this is iffmat: F 4.0000000 >> g40cond_as >> >> g40cond_as.fld01 >> >> >> >> The same data can be read correctly in Visit, however. Any ideas? >> >> Additionally, if this problem cannot be overcome, is there a way to take >> profile points using Visit or Matlab? >> >> Thank you for your help, >> >> Chris >> >> >> -- >> Christopher O. Mehrvarzi >> Paul Research Group >> Virginia Tech - Mechanical Engineering >> chrisom3 at vt.edu >> >> > > > -- > Christopher O. Mehrvarzi > Paul Research Group > Virginia Tech - Mechanical Engineering > chrisom3 at vt.edu > > -- Christopher O. Mehrvarzi Paul Research Group Virginia Tech - Mechanical Engineering chrisom3 at vt.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Sep 9 14:12:52 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 9 Sep 2013 14:12:52 -0500 Subject: [Nek5000-users] Problem reading binary .fld files into postnek In-Reply-To: References: Message-ID: Hi, Is it the same "error reading REA" problem? Can you send the terminal output you are getting and your base .rea file? You can send if off list, heisey at mcs.anl.gov Thanks Katie On Mon, Sep 9, 2013 at 1:11 PM, wrote: > Hi Neks, > > I apologize for the delayed response. Thank you for your suggestions. > > Paul -- my files are in .fld format. > > Kate -- I was using an older version of postnek. I compiled the latest > version on my computer and tried again, but I'm still running into > problems. > > Thank you for your time, > Chris > > > On Wed, Sep 4, 2013 at 2:46 PM, Christopher Mehrvarzi wrote: > >> Hi Paul, >> >> Thank you for your suggestions. I am using a standard .rea file and >> already had the flags at p66 and p67 set to 4 (the extension of my data >> is .fld) but the problem still occurs. I tried setting the flags to 6 >> anyways but still encountered the same problem. >> >> Chris >> >> >> On Wed, Sep 4, 2013 at 9:33 AM, Christopher Mehrvarzi wrote: >> >>> Hi Neks, >>> >>> I am having some issues importing my binary-type data into postnek. When >>> the files are imported into postnek, many of the elements are missing and >>> this is part of the message that appears in the terminal: >>> >>> >>> -Adobe-Helvetica-Medium-R-Normal--12-120-75-75-P-67-ISO8859-1 >>> NEKTON Version 2.6 >>> >>> I/O Error: No String Terminator sent to PRS >>> Enter Session Name (Default= g40cond_as >>> >>> I/O Error: No String Terminator sent to PRS >>> Beginning Session g40cond_as >>> >>> renaming SESSION.NAME SESSION.NAME~ >>> Session name:"g40cond_as >>> " >>> cp: /Users/chris/.nekdefaults: No such file or directory >>> renaming g40cond_as.plt01 g40cond_as.plt01~ >>> >>> LTRUNC: string: 80 >>> >>> LTRUNC: string: 28 >>> Wed Sep 4 09:30:51 EDT 2013 >>> I/O Error: No String Terminator sent to PRS >>> Reading geometry from >>> XYZ Min,Max: >>> -40.0000 40.0000 >>> -40.0000 40.0000 >>> 0.00000 1.00000 >>> 1 3017 1 TRYING TO READ BC >>> 7 3072 2 TRYING TO READ BC >>> 7 3072 3 TRYING TO READ BC >>> 7 3072 4 TRYING TO READ BC >>> 7 3072 5 TRYING TO READ BC >>> Error reading options in .REA file >>> >>> this is iffmat: F 4.0000000 >>> g40cond_as >>> >>> g40cond_as.fld01 >>> >>> >>> >>> The same data can be read correctly in Visit, however. Any ideas? >>> >>> Additionally, if this problem cannot be overcome, is there a way to take >>> profile points using Visit or Matlab? >>> >>> Thank you for your help, >>> >>> Chris >>> >>> >>> -- >>> Christopher O. Mehrvarzi >>> Paul Research Group >>> Virginia Tech - Mechanical Engineering >>> chrisom3 at vt.edu >>> >>> >> >> >> -- >> Christopher O. Mehrvarzi >> Paul Research Group >> Virginia Tech - Mechanical Engineering >> chrisom3 at vt.edu >> >> > > > -- > Christopher O. Mehrvarzi > Paul Research Group > Virginia Tech - Mechanical Engineering > chrisom3 at vt.edu > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Sep 11 09:31:21 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Sep 2013 10:31:21 -0400 Subject: [Nek5000-users] Running MOAB example Message-ID: Hello Neks, I am trying to run MOAB example with nek5000, but all the time which I am running, it gives me set of undefined reference error. I put an error with last part of my ./makenek pipe log below. What is wrong with my work? IODebugTrack.cpp:(.text+0xb74): undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' IODebugTrack.cpp:(.text+0xb7f): undefined reference to `std::basic_ostream >::operator<<(unsigned long)' IODebugTrack.cpp:(.text+0xb8c): undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' IODebugTrack.cpp:(.text+0xb97): undefined reference to `std::basic_ostream >::operator<<(unsigned long)' IODebugTrack.cpp:(.text+0xbd3): undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' IODebugTrack.cpp:(.text+0xbde): undefined reference to `std::basic_ostream >::operator<<(unsigned long)' IODebugTrack.cpp:(.text+0xbeb): undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' IODebugTrack.cpp:(.text+0xbf6): undefined reference to `std::basic_ostream >::operator<<(unsigned long)' IODebugTrack.cpp:(.text+0xc03): undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' IODebugTrack.cpp:(.text+0xc0e): undefined reference to `std::basic_ostream >::operator<<(unsigned long)' IODebugTrack.cpp:(.text+0xc1b): undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' IODebugTrack.cpp:(.text+0xc26): undefined reference to `std::basic_ostream >::operator<<(unsigned long)' IODebugTrack.cpp:(.text+0xc33): undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' IODebugTrack.cpp:(.text+0xc38): undefined reference to `std::basic_ostream >& std::endl >(std::basic_ostream >&)' IODebugTrack.cpp:(.text+0xc40): undefined reference to `std::basic_ostream >::operator<<(std::basic_ostream >& (*)(std::basic_ostream >&))' IODebugTrack.cpp:(.text+0xc50): undefined reference to `std::basic_ostream >::flush()' /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In function `moab::IODebugTrack::all_reduce()': IODebugTrack.cpp:(.text+0xd08): undefined reference to `MPI_Comm_size' IODebugTrack.cpp:(.text+0xdfe): undefined reference to `MPI_Gather' IODebugTrack.cpp:(.text+0x1080): undefined reference to `MPI_Gatherv' /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In function `__static_initialization_and_destruction_0(int, int)': IODebugTrack.cpp:(.text+0x1221): undefined reference to `std::ios_base::Init::Init()' IODebugTrack.cpp:(.text+0x1226): undefined reference to `std::ios_base::Init::~Init()' /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In function `std::list >::_M_insert(std::_List_iterator, moab::IODebugTrack::DRange const&)': IODebugTrack.cpp:(.text._ZNSt4listIN4moab12IODebugTrack6DRangeESaIS2_EE9_M_insertESt14_List_iteratorIS2_ERKS2_[std::list >::_M_insert(std::_List_iterator, moab::IODebugTrack::DRange const&)]+0x3a): undefined reference to `std::__detail::_List_node_base::_M_hook(std::__detail::_List_node_base*)' /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In function `__gnu_cxx::new_allocator >::deallocate(std::_List_node*, unsigned long)': IODebugTrack.cpp:(.text._ZN9__gnu_cxx13new_allocatorISt10_List_nodeIN4moab12IODebugTrack6DRangeEEE10deallocateEPS5_m[__gnu_cxx::new_allocator >::deallocate(std::_List_node*, unsigned long)]+0x1c): undefined reference to `operator delete(void*)' /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In function `__gnu_cxx::new_allocator::allocate(unsigned long, void const*)': IODebugTrack.cpp:(.text._ZN9__gnu_cxx13new_allocatorIN4moab12IODebugTrack6DRangeEE8allocateEmPKv[__gnu_cxx::new_allocator::allocate(unsigned long, void const*)]+0x2c): undefined reference to `std::__throw_bad_alloc()' IODebugTrack.cpp:(.text._ZN9__gnu_cxx13new_allocatorIN4moab12IODebugTrack6DRangeEE8allocateEmPKv[__gnu_cxx::new_allocator::allocate(unsigned long, void const*)]+0x45): undefined reference to `operator new(unsigned long)' /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In function `__gnu_cxx::new_allocator::deallocate(moab::IODebugTrack::DRange*, unsigned long)': IODebugTrack.cpp:(.text._ZN9__gnu_cxx13new_allocatorIN4moab12IODebugTrack6DRangeEE10deallocateEPS3_m[__gnu_cxx::new_allocator::deallocate(moab::IODebugTrack::DRange*, unsigned long)]+0x1c): undefined reference to `operator delete(void*)' /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In function `__gnu_cxx::new_allocator >::allocate(unsigned long, void const*)': IODebugTrack.cpp:(.text._ZN9__gnu_cxx13new_allocatorISt10_List_nodeIN4moab12IODebugTrack6DRangeEEE8allocateEmPKv[__gnu_cxx::new_allocator >::allocate(unsigned long, void const*)]+0x2c): undefined reference to `std::__throw_bad_alloc()' IODebugTrack.cpp:(.text._ZN9__gnu_cxx13new_allocatorISt10_List_nodeIN4moab12IODebugTrack6DRangeEEE8allocateEmPKv[__gnu_cxx::new_allocator >::allocate(unsigned long, void const*)]+0x46): undefined reference to `operator new(unsigned long)' /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o):(.eh_frame+0x24b): undefined reference to `__gxx_personality_v0' /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(OrientedBox.o): In function `moab::operator<<(std::basic_ostream >&, moab::OrientedBox const&)': OrientedBox.cpp:(.text+0x97): undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' OrientedBox.cpp:(.text+0xaf): undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' OrientedBox.cpp:(.text+0xbc): undefined reference to `std::basic_ostream >::operator<<(double)' OrientedBox.cpp:(.text+0xc9): undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' OrientedBox.cpp:(.text+0xe1): undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' OrientedBox.cpp:(.text+0xee): undefined reference to `std::basic_ostream >::operator<<(double)' OrientedBox.cpp:(.text+0xfb): undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' OrientedBox.cpp:(.text+0x113): undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' OrientedBox.cpp:(.text+0x120): undefined reference to `std::basic_ostream >::operator<<(double)' /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(OrientedBox.o): In function `__static_initialization_and_destruction_0(int, int)': OrientedBox.cpp:(.text+0x3aaf): undefined reference to `std::ios_base::Init::Init()' OrientedBox.cpp:(.text+0x3ab4): undefined reference to `std::ios_base::Init::~Init()' /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(OrientedBox.o): In function `moab::ErrorCode moab::EigenDecomp(moab::Matrix3 const&, double*, moab::CartVect*)': OrientedBox.cpp:(.text._ZN4moab11EigenDecompINS_7Matrix3ENS_8CartVectEEENS_9ErrorCodeERKT_PdPT0_[moab::ErrorCode moab::EigenDecomp(moab::Matrix3 const&, double*, moab::CartVect*)]+0xb7f): undefined reference to `std::cerr' OrientedBox.cpp:(.text._ZN4moab11EigenDecompINS_7Matrix3ENS_8CartVectEEENS_9ErrorCodeERKT_PdPT0_[moab::ErrorCode moab::EigenDecomp(moab::Matrix3 const&, double*, moab::CartVect*)]+0xb84): undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' OrientedBox.cpp:(.text._ZN4moab11EigenDecompINS_7Matrix3ENS_8CartVectEEENS_9ErrorCodeERKT_PdPT0_[moab::ErrorCode moab::EigenDecomp(moab::Matrix3 const&, double*, moab::CartVect*)]+0xb89): undefined reference to `std::basic_ostream >& std::endl >(std::basic_ostream >&)' OrientedBox.cpp:(.text._ZN4moab11EigenDecompINS_7Matrix3ENS_8CartVectEEENS_9ErrorCodeERKT_PdPT0_[moab::ErrorCode moab::EigenDecomp(moab::Matrix3 const&, double*, moab::CartVect*)]+0xb91): undefined reference to `std::basic_ostream >::operator<<(std::basic_ostream >& (*)(std::basic_ostream >&))' /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(OrientedBox.o):(.eh_frame+0x22f): undefined reference to `__gxx_personality_v0' collect2: ld returned 1 exit status make: *** [nek5000] Error 1 Thanks, Ami -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Sep 11 09:47:00 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Sep 2013 09:47:00 -0500 Subject: [Nek5000-users] Running MOAB example In-Reply-To: References: Message-ID: Hi Ami, That's the C++ runtime. You have two options: 1. Link with the C++ compiler; in this case, you'll have to explicitly add the fortran runtime libraries to the link statement, which is most easily done by adding it to USR_LFLAGS in makenek. Compiler documents often tell you which libraries implement the fortran runtime, usually in a section about inter-language linking. 2. Add the C++ std libs to USR_LFLAGS. The trunk/nek/makenek file has a few examples of this method for gnu/intel/pgi. Sometimes, like on BG/x, it can be difficult to figure out what all comprises the C++ runtime, which is why I list 1. above. - tim On 09/11/2013 09:31 AM, nek5000-users at lists.mcs.anl.gov wrote: > Hello Neks, > > I am trying to run MOAB example with nek5000, but all the time which I am running, it gives me set of undefined > reference error. I put an error with last part of my ./makenek pipe log below. > What is wrong with my work? > > IODebugTrack.cpp:(.text+0xb74): undefined reference to `std::basic_ostream >& > std::operator<< >(std::basic_ostream >&, char const*)' > IODebugTrack.cpp:(.text+0xb7f): undefined reference to `std::basic_ostream > >::operator<<(unsigned long)' > IODebugTrack.cpp:(.text+0xb8c): undefined reference to `std::basic_ostream >& > std::operator<< >(std::basic_ostream >&, char const*)' > IODebugTrack.cpp:(.text+0xb97): undefined reference to `std::basic_ostream > >::operator<<(unsigned long)' > IODebugTrack.cpp:(.text+0xbd3): undefined reference to `std::basic_ostream >& > std::operator<< >(std::basic_ostream >&, char const*)' > IODebugTrack.cpp:(.text+0xbde): undefined reference to `std::basic_ostream > >::operator<<(unsigned long)' > IODebugTrack.cpp:(.text+0xbeb): undefined reference to `std::basic_ostream >& > std::operator<< >(std::basic_ostream >&, char const*)' > IODebugTrack.cpp:(.text+0xbf6): undefined reference to `std::basic_ostream > >::operator<<(unsigned long)' > IODebugTrack.cpp:(.text+0xc03): undefined reference to `std::basic_ostream >& > std::operator<< >(std::basic_ostream >&, char const*)' > IODebugTrack.cpp:(.text+0xc0e): undefined reference to `std::basic_ostream > >::operator<<(unsigned long)' > IODebugTrack.cpp:(.text+0xc1b): undefined reference to `std::basic_ostream >& > std::operator<< >(std::basic_ostream >&, char const*)' > IODebugTrack.cpp:(.text+0xc26): undefined reference to `std::basic_ostream > >::operator<<(unsigned long)' > IODebugTrack.cpp:(.text+0xc33): undefined reference to `std::basic_ostream >& > std::operator<< >(std::basic_ostream >&, char const*)' > IODebugTrack.cpp:(.text+0xc38): undefined reference to `std::basic_ostream >& > std::endl >(std::basic_ostream >&)' > IODebugTrack.cpp:(.text+0xc40): undefined reference to `std::basic_ostream > >::operator<<(std::basic_ostream >& (*)(std::basic_ostream >&))' > IODebugTrack.cpp:(.text+0xc50): undefined reference to `std::basic_ostream >::flush()' > /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In function `moab::IODebugTrack::all_reduce()': > IODebugTrack.cpp:(.text+0xd08): undefined reference to `MPI_Comm_size' > IODebugTrack.cpp:(.text+0xdfe): undefined reference to `MPI_Gather' > IODebugTrack.cpp:(.text+0x1080): undefined reference to `MPI_Gatherv' > /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In function > `__static_initialization_and_destruction_0(int, int)': > IODebugTrack.cpp:(.text+0x1221): undefined reference to `std::ios_base::Init::Init()' > IODebugTrack.cpp:(.text+0x1226): undefined reference to `std::ios_base::Init::~Init()' > /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In function `std::list std::allocator >::_M_insert(std::_List_iterator, > moab::IODebugTrack::DRange const&)': > IODebugTrack.cpp:(.text._ZNSt4listIN4moab12IODebugTrack6DRangeESaIS2_EE9_M_insertESt14_List_iteratorIS2_ERKS2_[std::list std::allocator >::_M_insert(std::_List_iterator, > moab::IODebugTrack::DRange const&)]+0x3a): undefined reference to > `std::__detail::_List_node_base::_M_hook(std::__detail::_List_node_base*)' > /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In function > `__gnu_cxx::new_allocator > >::deallocate(std::_List_node*, unsigned long)': > IODebugTrack.cpp:(.text._ZN9__gnu_cxx13new_allocatorISt10_List_nodeIN4moab12IODebugTrack6DRangeEEE10deallocateEPS5_m[__gnu_cxx::new_allocator > >::deallocate(std::_List_node*, unsigned long)]+0x1c): undefined reference to `operator > delete(void*)' > /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In function > `__gnu_cxx::new_allocator::allocate(unsigned long, void const*)': > IODebugTrack.cpp:(.text._ZN9__gnu_cxx13new_allocatorIN4moab12IODebugTrack6DRangeEE8allocateEmPKv[__gnu_cxx::new_allocator::allocate(unsigned > long, void const*)]+0x2c): undefined reference to `std::__throw_bad_alloc()' > IODebugTrack.cpp:(.text._ZN9__gnu_cxx13new_allocatorIN4moab12IODebugTrack6DRangeEE8allocateEmPKv[__gnu_cxx::new_allocator::allocate(unsigned > long, void const*)]+0x45): undefined reference to `operator new(unsigned long)' > /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In function > `__gnu_cxx::new_allocator::deallocate(moab::IODebugTrack::DRange*, unsigned long)': > IODebugTrack.cpp:(.text._ZN9__gnu_cxx13new_allocatorIN4moab12IODebugTrack6DRangeEE10deallocateEPS3_m[__gnu_cxx::new_allocator::deallocate(moab::IODebugTrack::DRange*, > unsigned long)]+0x1c): undefined reference to `operator delete(void*)' > /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In function > `__gnu_cxx::new_allocator >::allocate(unsigned long, void const*)': > IODebugTrack.cpp:(.text._ZN9__gnu_cxx13new_allocatorISt10_List_nodeIN4moab12IODebugTrack6DRangeEEE8allocateEmPKv[__gnu_cxx::new_allocator > >::allocate(unsigned long, void const*)]+0x2c): undefined reference to `std::__throw_bad_alloc()' > IODebugTrack.cpp:(.text._ZN9__gnu_cxx13new_allocatorISt10_List_nodeIN4moab12IODebugTrack6DRangeEEE8allocateEmPKv[__gnu_cxx::new_allocator > >::allocate(unsigned long, void const*)]+0x46): undefined reference to `operator new(unsigned long)' > /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o):(.eh_frame+0x24b): undefined reference to > `__gxx_personality_v0' > /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(OrientedBox.o): In function > `moab::operator<<(std::basic_ostream >&, moab::OrientedBox const&)': > OrientedBox.cpp:(.text+0x97): undefined reference to `std::basic_ostream >& std::operator<< > >(std::basic_ostream >&, char const*)' > OrientedBox.cpp:(.text+0xaf): undefined reference to `std::basic_ostream >& std::operator<< > >(std::basic_ostream >&, char const*)' > OrientedBox.cpp:(.text+0xbc): undefined reference to `std::basic_ostream >::operator<<(double)' > OrientedBox.cpp:(.text+0xc9): undefined reference to `std::basic_ostream >& std::operator<< > >(std::basic_ostream >&, char const*)' > OrientedBox.cpp:(.text+0xe1): undefined reference to `std::basic_ostream >& std::operator<< > >(std::basic_ostream >&, char const*)' > OrientedBox.cpp:(.text+0xee): undefined reference to `std::basic_ostream >::operator<<(double)' > OrientedBox.cpp:(.text+0xfb): undefined reference to `std::basic_ostream >& std::operator<< > >(std::basic_ostream >&, char const*)' > OrientedBox.cpp:(.text+0x113): undefined reference to `std::basic_ostream >& > std::operator<< >(std::basic_ostream >&, char const*)' > OrientedBox.cpp:(.text+0x120): undefined reference to `std::basic_ostream > >::operator<<(double)' > /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(OrientedBox.o): In function > `__static_initialization_and_destruction_0(int, int)': > OrientedBox.cpp:(.text+0x3aaf): undefined reference to `std::ios_base::Init::Init()' > OrientedBox.cpp:(.text+0x3ab4): undefined reference to `std::ios_base::Init::~Init()' > /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(OrientedBox.o): In function `moab::ErrorCode > moab::EigenDecomp(moab::Matrix3 const&, double*, moab::CartVect*)': > OrientedBox.cpp:(.text._ZN4moab11EigenDecompINS_7Matrix3ENS_8CartVectEEENS_9ErrorCodeERKT_PdPT0_[moab::ErrorCode > moab::EigenDecomp(moab::Matrix3 const&, double*, moab::CartVect*)]+0xb7f): undefined > reference to `std::cerr' > OrientedBox.cpp:(.text._ZN4moab11EigenDecompINS_7Matrix3ENS_8CartVectEEENS_9ErrorCodeERKT_PdPT0_[moab::ErrorCode > moab::EigenDecomp(moab::Matrix3 const&, double*, moab::CartVect*)]+0xb84): undefined > reference to `std::basic_ostream >& std::operator<< > >(std::basic_ostream >&, char const*)' > OrientedBox.cpp:(.text._ZN4moab11EigenDecompINS_7Matrix3ENS_8CartVectEEENS_9ErrorCodeERKT_PdPT0_[moab::ErrorCode > moab::EigenDecomp(moab::Matrix3 const&, double*, moab::CartVect*)]+0xb89): undefined > reference to `std::basic_ostream >& std::endl > >(std::basic_ostream >&)' > OrientedBox.cpp:(.text._ZN4moab11EigenDecompINS_7Matrix3ENS_8CartVectEEENS_9ErrorCodeERKT_PdPT0_[moab::ErrorCode > moab::EigenDecomp(moab::Matrix3 const&, double*, moab::CartVect*)]+0xb91): undefined > reference to `std::basic_ostream >::operator<<(std::basic_ostream std::char_traits >& (*)(std::basic_ostream >&))' > /home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(OrientedBox.o):(.eh_frame+0x22f): undefined reference to > `__gxx_personality_v0' > collect2: ld returned 1 exit status > make: *** [nek5000] Error 1 > > Thanks, > Ami > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -- ================================================================ "You will keep in perfect peace him whose mind is steadfast, because he trusts in you." Isaiah 26:3 Tim Tautges Argonne National Laboratory (tautges at mcs.anl.gov) (telecommuting from UW-Madison) phone (gvoice): (608) 354-1459 1500 Engineering Dr. fax: (608) 263-4499 Madison, WI 53706 From nek5000-users at lists.mcs.anl.gov Wed Sep 11 10:11:04 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Sep 2013 11:11:04 -0400 Subject: [Nek5000-users] Running MOAB example In-Reply-To: References: Message-ID: Thanks for your answer, to make sure I have added libraries to makenek ''USR_LFLAGS="-lmpi_cxx -lstdc++" which I'm getting same error,so you mean I need to add appropriate fortran library to USR_LFLAGS? Thanks, Ami On Wed, Sep 11, 2013 at 10:47 AM, wrote: > Hi Ami, > That's the C++ runtime. You have two options: > 1. Link with the C++ compiler; in this case, you'll have to explicitly add > the fortran runtime libraries to the link statement, which is most easily > done by adding it to USR_LFLAGS in makenek. Compiler documents often tell > you which libraries implement the fortran runtime, usually in a section > about inter-language linking. > > 2. Add the C++ std libs to USR_LFLAGS. The trunk/nek/makenek file has a > few examples of this method for gnu/intel/pgi. Sometimes, like on BG/x, it > can be difficult to figure out what all comprises the C++ runtime, which is > why I list 1. above. > > - tim > > > On 09/11/2013 09:31 AM, nek5000-users at lists.mcs.anl.**govwrote: > >> Hello Neks, >> >> I am trying to run MOAB example with nek5000, but all the time which I am >> running, it gives me set of undefined >> reference error. I put an error with last part of my ./makenek pipe log >> below. >> What is wrong with my work? >> >> IODebugTrack.cpp:(.text+0xb74)**: undefined reference to >> `std::basic_ostream >& >> std::operator<< >(std::basic_ostream> std::char_traits >&, char const*)' >> IODebugTrack.cpp:(.text+0xb7f)**: undefined reference to >> `std::basic_ostream >> >::operator<<(unsigned long)' >> IODebugTrack.cpp:(.text+0xb8c)**: undefined reference to >> `std::basic_ostream >& >> std::operator<< >(std::basic_ostream> std::char_traits >&, char const*)' >> IODebugTrack.cpp:(.text+0xb97)**: undefined reference to >> `std::basic_ostream >> >::operator<<(unsigned long)' >> IODebugTrack.cpp:(.text+0xbd3)**: undefined reference to >> `std::basic_ostream >& >> std::operator<< >(std::basic_ostream> std::char_traits >&, char const*)' >> IODebugTrack.cpp:(.text+0xbde)**: undefined reference to >> `std::basic_ostream >> >::operator<<(unsigned long)' >> IODebugTrack.cpp:(.text+0xbeb)**: undefined reference to >> `std::basic_ostream >& >> std::operator<< >(std::basic_ostream> std::char_traits >&, char const*)' >> IODebugTrack.cpp:(.text+0xbf6)**: undefined reference to >> `std::basic_ostream >> >::operator<<(unsigned long)' >> IODebugTrack.cpp:(.text+0xc03)**: undefined reference to >> `std::basic_ostream >& >> std::operator<< >(std::basic_ostream> std::char_traits >&, char const*)' >> IODebugTrack.cpp:(.text+0xc0e)**: undefined reference to >> `std::basic_ostream >> >::operator<<(unsigned long)' >> IODebugTrack.cpp:(.text+0xc1b)**: undefined reference to >> `std::basic_ostream >& >> std::operator<< >(std::basic_ostream> std::char_traits >&, char const*)' >> IODebugTrack.cpp:(.text+0xc26)**: undefined reference to >> `std::basic_ostream >> >::operator<<(unsigned long)' >> IODebugTrack.cpp:(.text+0xc33)**: undefined reference to >> `std::basic_ostream >& >> std::operator<< >(std::basic_ostream> std::char_traits >&, char const*)' >> IODebugTrack.cpp:(.text+0xc38)**: undefined reference to >> `std::basic_ostream >& >> std::endl >(std::basic_ostream> std::char_traits >&)' >> IODebugTrack.cpp:(.text+0xc40)**: undefined reference to >> `std::basic_ostream >> >::operator<<(std::basic_**ostream >& >> (*)(std::basic_ostream >&))' >> IODebugTrack.cpp:(.text+0xc50)**: undefined reference to >> `std::basic_ostream >::flush()' >> /home/amirreza/Amirreza/moab-**4.6.0/gcc/lib/libMOAB.a(**IODebugTrack.o): >> In function `moab::IODebugTrack::all_**reduce()': >> IODebugTrack.cpp:(.text+0xd08)**: undefined reference to `MPI_Comm_size' >> IODebugTrack.cpp:(.text+0xdfe)**: undefined reference to `MPI_Gather' >> IODebugTrack.cpp:(.text+**0x1080): undefined reference to `MPI_Gatherv' >> /home/amirreza/Amirreza/moab-**4.6.0/gcc/lib/libMOAB.a(**IODebugTrack.o): >> In function >> `__static_initialization_and_**destruction_0(int, int)': >> IODebugTrack.cpp:(.text+**0x1221): undefined reference to >> `std::ios_base::Init::Init()' >> IODebugTrack.cpp:(.text+**0x1226): undefined reference to >> `std::ios_base::Init::~Init()' >> /home/amirreza/Amirreza/moab-**4.6.0/gcc/lib/libMOAB.a(**IODebugTrack.o): >> In function `std::list> std::allocator >::_M_insert(std::_List_** >> iterator, >> moab::IODebugTrack::DRange const&)': >> IODebugTrack.cpp:(.text._**ZNSt4listIN4moab12IODebugTrack** >> 6DRangeESaIS2_EE9_M_**insertESt14_List_iteratorIS2_** >> ERKS2_[std::list> std::allocator >::_M_insert(std::_List_** >> iterator, >> moab::IODebugTrack::DRange const&)]+0x3a): undefined reference to >> `std::__detail::_List_node_**base::_M_hook(std::__detail::_** >> List_node_base*)' >> /home/amirreza/Amirreza/moab-**4.6.0/gcc/lib/libMOAB.a(**IODebugTrack.o): >> In function >> `__gnu_cxx::new_allocator >> >::deallocate(std::_List_node<**moab::IODebugTrack::DRange>*, unsigned >> long)': >> IODebugTrack.cpp:(.text._ZN9__**gnu_cxx13new_allocatorISt10_**List_** >> nodeIN4moab12IODebugTrack6DRan**geEEE10deallocateEPS5_m[__gnu_** >> cxx::new_allocator >> >::deallocate(std::_List_node<**moab::IODebugTrack::DRange>*, unsigned >> long)]+0x1c): undefined reference to `operator >> delete(void*)' >> /home/amirreza/Amirreza/moab-**4.6.0/gcc/lib/libMOAB.a(**IODebugTrack.o): >> In function >> `__gnu_cxx::new_allocator<**moab::IODebugTrack::DRange>::**allocate(unsigned >> long, void const*)': >> IODebugTrack.cpp:(.text._ZN9__**gnu_cxx13new_** >> allocatorIN4moab12IODebugTrack**6DRangeEE8allocateEmPKv[__gnu_** >> cxx::new_allocator::**allocate(unsigned >> long, void const*)]+0x2c): undefined reference to >> `std::__throw_bad_alloc()' >> IODebugTrack.cpp:(.text._ZN9__**gnu_cxx13new_** >> allocatorIN4moab12IODebugTrack**6DRangeEE8allocateEmPKv[__gnu_** >> cxx::new_allocator::**allocate(unsigned >> long, void const*)]+0x45): undefined reference to `operator new(unsigned >> long)' >> /home/amirreza/Amirreza/moab-**4.6.0/gcc/lib/libMOAB.a(**IODebugTrack.o): >> In function >> `__gnu_cxx::new_allocator<**moab::IODebugTrack::DRange>::** >> deallocate(moab::IODebugTrack:**:DRange*, unsigned long)': >> IODebugTrack.cpp:(.text._ZN9__**gnu_cxx13new_** >> allocatorIN4moab12IODebugTrack**6DRangeEE10deallocateEPS3_m[__** >> gnu_cxx::new_allocator::** >> deallocate(moab::IODebugTrack:**:DRange*, >> unsigned long)]+0x1c): undefined reference to `operator delete(void*)' >> /home/amirreza/Amirreza/moab-**4.6.0/gcc/lib/libMOAB.a(**IODebugTrack.o): >> In function >> `__gnu_cxx::new_allocator >> >::allocate(unsigned long, void const*)': >> IODebugTrack.cpp:(.text._ZN9__**gnu_cxx13new_allocatorISt10_**List_** >> nodeIN4moab12IODebugTrack6DRan**geEEE8allocateEmPKv[__gnu_cxx:** >> :new_allocator >> >::allocate(unsigned long, void const*)]+0x2c): undefined reference to >> `std::__throw_bad_alloc()' >> IODebugTrack.cpp:(.text._ZN9__**gnu_cxx13new_allocatorISt10_**List_** >> nodeIN4moab12IODebugTrack6DRan**geEEE8allocateEmPKv[__gnu_cxx:** >> :new_allocator >> >::allocate(unsigned long, void const*)]+0x46): undefined reference to >> `operator new(unsigned long)' >> /home/amirreza/Amirreza/moab-**4.6.0/gcc/lib/libMOAB.a(** >> IODebugTrack.o):(.eh_frame+**0x24b): undefined reference to >> `__gxx_personality_v0' >> /home/amirreza/Amirreza/moab-**4.6.0/gcc/lib/libMOAB.a(**OrientedBox.o): >> In function >> `moab::operator<<(std::basic_**ostream >&, >> moab::OrientedBox const&)': >> OrientedBox.cpp:(.text+0x97): undefined reference to >> `std::basic_ostream >& std::operator<< >> >(std::basic_ostream >> >&, char const*)' >> OrientedBox.cpp:(.text+0xaf): undefined reference to >> `std::basic_ostream >& std::operator<< >> >(std::basic_ostream >> >&, char const*)' >> OrientedBox.cpp:(.text+0xbc): undefined reference to >> `std::basic_ostream >::operator<<(double)' >> OrientedBox.cpp:(.text+0xc9): undefined reference to >> `std::basic_ostream >& std::operator<< >> >(std::basic_ostream >> >&, char const*)' >> OrientedBox.cpp:(.text+0xe1): undefined reference to >> `std::basic_ostream >& std::operator<< >> >(std::basic_ostream >> >&, char const*)' >> OrientedBox.cpp:(.text+0xee): undefined reference to >> `std::basic_ostream >::operator<<(double)' >> OrientedBox.cpp:(.text+0xfb): undefined reference to >> `std::basic_ostream >& std::operator<< >> >(std::basic_ostream >> >&, char const*)' >> OrientedBox.cpp:(.text+0x113): undefined reference to >> `std::basic_ostream >& >> std::operator<< >(std::basic_ostream> std::char_traits >&, char const*)' >> OrientedBox.cpp:(.text+0x120): undefined reference to >> `std::basic_ostream >> >::operator<<(double)' >> /home/amirreza/Amirreza/moab-**4.6.0/gcc/lib/libMOAB.a(**OrientedBox.o): >> In function >> `__static_initialization_and_**destruction_0(int, int)': >> OrientedBox.cpp:(.text+0x3aaf)**: undefined reference to >> `std::ios_base::Init::Init()' >> OrientedBox.cpp:(.text+0x3ab4)**: undefined reference to >> `std::ios_base::Init::~Init()' >> /home/amirreza/Amirreza/moab-**4.6.0/gcc/lib/libMOAB.a(**OrientedBox.o): >> In function `moab::ErrorCode >> moab::EigenDecomp(moab::Matrix3 const&, >> double*, moab::CartVect*)': >> OrientedBox.cpp:(.text._**ZN4moab11EigenDecompINS_** >> 7Matrix3ENS_8CartVectEEENS_**9ErrorCodeERKT_PdPT0_[moab::**ErrorCode >> moab::EigenDecomp(moab::Matrix3 const&, >> double*, moab::CartVect*)]+0xb7f): undefined >> reference to `std::cerr' >> OrientedBox.cpp:(.text._**ZN4moab11EigenDecompINS_** >> 7Matrix3ENS_8CartVectEEENS_**9ErrorCodeERKT_PdPT0_[moab::**ErrorCode >> moab::EigenDecomp(moab::Matrix3 const&, >> double*, moab::CartVect*)]+0xb84): undefined >> reference to `std::basic_ostream >& >> std::operator<< >> >(std::basic_ostream >&, char const*)' >> OrientedBox.cpp:(.text._**ZN4moab11EigenDecompINS_** >> 7Matrix3ENS_8CartVectEEENS_**9ErrorCodeERKT_PdPT0_[moab::**ErrorCode >> moab::EigenDecomp(moab::Matrix3 const&, >> double*, moab::CartVect*)]+0xb89): undefined >> reference to `std::basic_ostream >& >> std::endl >> >(std::basic_ostream >&)' >> OrientedBox.cpp:(.text._**ZN4moab11EigenDecompINS_** >> 7Matrix3ENS_8CartVectEEENS_**9ErrorCodeERKT_PdPT0_[moab::**ErrorCode >> moab::EigenDecomp(moab::Matrix3 const&, >> double*, moab::CartVect*)]+0xb91): undefined >> reference to `std::basic_ostream >> >::operator<<(std::basic_**ostream> std::char_traits >& (*)(std::basic_ostream> std::char_traits >&))' >> /home/amirreza/Amirreza/moab-**4.6.0/gcc/lib/libMOAB.a(** >> OrientedBox.o):(.eh_frame+**0x22f): undefined reference to >> `__gxx_personality_v0' >> collect2: ld returned 1 exit status >> make: *** [nek5000] Error 1 >> >> Thanks, >> Ami >> >> >> ______________________________**_________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.**gov >> https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users >> >> > -- > ==============================**==============================**==== > "You will keep in perfect peace him whose mind is > steadfast, because he trusts in you." Isaiah 26:3 > > Tim Tautges Argonne National Laboratory > (tautges at mcs.anl.gov) (telecommuting from UW-Madison) > phone (gvoice): (608) 354-1459 1500 Engineering Dr. > fax: (608) 263-4499 Madison, WI 53706 > > ______________________________**_________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.**gov > https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Sep 11 11:05:44 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Sep 2013 11:05:44 -0500 Subject: [Nek5000-users] Running MOAB example In-Reply-To: References: Message-ID: It depends which compiler you're using. Are you using gnu? Please send complete compile output. - tim On 09/11/2013 10:11 AM, nek5000-users at lists.mcs.anl.gov wrote: > Thanks for your answer, to make sure I have added libraries to makenek ''USR_LFLAGS="-lmpi_cxx -lstdc++" which I'm > getting same error,so you mean I need to add appropriate fortran library to USR_LFLAGS? > > Thanks, > Ami > > > On Wed, Sep 11, 2013 at 10:47 AM, > wrote: > > Hi Ami, > That's the C++ runtime. You have two options: > 1. Link with the C++ compiler; in this case, you'll have to explicitly add the fortran runtime libraries to the link > statement, which is most easily done by adding it to USR_LFLAGS in makenek. Compiler documents often tell you which > libraries implement the fortran runtime, usually in a section about inter-language linking. > > 2. Add the C++ std libs to USR_LFLAGS. The trunk/nek/makenek file has a few examples of this method for > gnu/intel/pgi. Sometimes, like on BG/x, it can be difficult to figure out what all comprises the C++ runtime, which > is why I list 1. above. > > - tim > > > On 09/11/2013 09:31 AM, nek5000-users at lists.mcs.anl.__gov wrote: > > Hello Neks, > > I am trying to run MOAB example with nek5000, but all the time which I am running, it gives me set of undefined > reference error. I put an error with last part of my ./makenek pipe log below. > What is wrong with my work? > > IODebugTrack.cpp:(.text+0xb74)__: undefined reference to `std::basic_ostream >& > std::operator<< >(std::basic_ostream >&, char const*)' > IODebugTrack.cpp:(.text+0xb7f)__: undefined reference to `std::basic_ostream > >::operator<<(unsigned long)' > IODebugTrack.cpp:(.text+0xb8c)__: undefined reference to `std::basic_ostream >& > std::operator<< >(std::basic_ostream >&, char const*)' > IODebugTrack.cpp:(.text+0xb97)__: undefined reference to `std::basic_ostream > >::operator<<(unsigned long)' > IODebugTrack.cpp:(.text+0xbd3)__: undefined reference to `std::basic_ostream >& > std::operator<< >(std::basic_ostream >&, char const*)' > IODebugTrack.cpp:(.text+0xbde)__: undefined reference to `std::basic_ostream > >::operator<<(unsigned long)' > IODebugTrack.cpp:(.text+0xbeb)__: undefined reference to `std::basic_ostream >& > std::operator<< >(std::basic_ostream >&, char const*)' > IODebugTrack.cpp:(.text+0xbf6)__: undefined reference to `std::basic_ostream > >::operator<<(unsigned long)' > IODebugTrack.cpp:(.text+0xc03)__: undefined reference to `std::basic_ostream >& > std::operator<< >(std::basic_ostream >&, char const*)' > IODebugTrack.cpp:(.text+0xc0e)__: undefined reference to `std::basic_ostream > >::operator<<(unsigned long)' > IODebugTrack.cpp:(.text+0xc1b)__: undefined reference to `std::basic_ostream >& > std::operator<< >(std::basic_ostream >&, char const*)' > IODebugTrack.cpp:(.text+0xc26)__: undefined reference to `std::basic_ostream > >::operator<<(unsigned long)' > IODebugTrack.cpp:(.text+0xc33)__: undefined reference to `std::basic_ostream >& > std::operator<< >(std::basic_ostream >&, char const*)' > IODebugTrack.cpp:(.text+0xc38)__: undefined reference to `std::basic_ostream >& > std::endl >(std::basic_ostream >&)' > IODebugTrack.cpp:(.text+0xc40)__: undefined reference to `std::basic_ostream > >::operator<<(std::basic___ostream >& (*)(std::basic_ostream std::char_traits >&))' > IODebugTrack.cpp:(.text+0xc50)__: undefined reference to `std::basic_ostream > >::flush()' > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In function > `moab::IODebugTrack::all___reduce()': > IODebugTrack.cpp:(.text+0xd08)__: undefined reference to `MPI_Comm_size' > IODebugTrack.cpp:(.text+0xdfe)__: undefined reference to `MPI_Gather' > IODebugTrack.cpp:(.text+__0x1080): undefined reference to `MPI_Gatherv' > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In function > `__static_initialization_and___destruction_0(int, int)': > IODebugTrack.cpp:(.text+__0x1221): undefined reference to `std::ios_base::Init::Init()' > IODebugTrack.cpp:(.text+__0x1226): undefined reference to `std::ios_base::Init::~Init()' > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In function > `std::list std::allocator >::_M_insert(std::_List___iterator, > moab::IODebugTrack::DRange const&)': > IODebugTrack.cpp:(.text.___ZNSt4listIN4moab12IODebugTrack__6DRangeESaIS2_EE9_M___insertESt14_List_iteratorIS2___ERKS2_[std::list std::allocator >::_M_insert(std::_List___iterator, > moab::IODebugTrack::DRange const&)]+0x3a): undefined reference to > `std::__detail::_List_node___base::_M_hook(std::__detail::___List_node_base*)' > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In function > `__gnu_cxx::new_allocator > >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, unsigned long)': > IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE10deallocateEPS5_m[__gnu___cxx::new_allocator > >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, unsigned long)]+0x1c): undefined reference to > `operator > delete(void*)' > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In function > `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__allocate(unsigned long, void const*)': > IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned > long, void const*)]+0x2c): undefined reference to `std::__throw_bad_alloc()' > IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned > long, void const*)]+0x45): undefined reference to `operator new(unsigned long)' > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In function > `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__deallocate(moab::IODebugTrack:__:DRange*, unsigned > long)': > IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE10deallocateEPS3_m[____gnu_cxx::new_allocator::__deallocate(moab::IODebugTrack:__:DRange*, > unsigned long)]+0x1c): undefined reference to `operator delete(void*)' > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In function > `__gnu_cxx::new_allocator >::allocate(unsigned long, void const*)': > IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator > >::allocate(unsigned long, void const*)]+0x2c): undefined reference to `std::__throw_bad_alloc()' > IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator > >::allocate(unsigned long, void const*)]+0x46): undefined reference to `operator new(unsigned long)' > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o):(.eh_frame+__0x24b): undefined reference to > `__gxx_personality_v0' > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In function > `moab::operator<<(std::basic___ostream >&, moab::OrientedBox const&)': > OrientedBox.cpp:(.text+0x97): undefined reference to `std::basic_ostream >& > std::operator<< > >(std::basic_ostream >&, char const*)' > OrientedBox.cpp:(.text+0xaf): undefined reference to `std::basic_ostream >& > std::operator<< > >(std::basic_ostream >&, char const*)' > OrientedBox.cpp:(.text+0xbc): undefined reference to `std::basic_ostream > >::operator<<(double)' > OrientedBox.cpp:(.text+0xc9): undefined reference to `std::basic_ostream >& > std::operator<< > >(std::basic_ostream >&, char const*)' > OrientedBox.cpp:(.text+0xe1): undefined reference to `std::basic_ostream >& > std::operator<< > >(std::basic_ostream >&, char const*)' > OrientedBox.cpp:(.text+0xee): undefined reference to `std::basic_ostream > >::operator<<(double)' > OrientedBox.cpp:(.text+0xfb): undefined reference to `std::basic_ostream >& > std::operator<< > >(std::basic_ostream >&, char const*)' > OrientedBox.cpp:(.text+0x113): undefined reference to `std::basic_ostream >& > std::operator<< >(std::basic_ostream >&, char const*)' > OrientedBox.cpp:(.text+0x120): undefined reference to `std::basic_ostream > >::operator<<(double)' > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In function > `__static_initialization_and___destruction_0(int, int)': > OrientedBox.cpp:(.text+0x3aaf)__: undefined reference to `std::ios_base::Init::Init()' > OrientedBox.cpp:(.text+0x3ab4)__: undefined reference to `std::ios_base::Init::~Init()' > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In function `moab::ErrorCode > moab::EigenDecomp(moab::Matrix3 const&, double*, moab::CartVect*)': > OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode > moab::EigenDecomp(moab::Matrix3 const&, double*, moab::CartVect*)]+0xb7f): > undefined > reference to `std::cerr' > OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode > moab::EigenDecomp(moab::Matrix3 const&, double*, moab::CartVect*)]+0xb84): > undefined > reference to `std::basic_ostream >& std::operator<< > >(std::basic_ostream >&, char const*)' > OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode > moab::EigenDecomp(moab::Matrix3 const&, double*, moab::CartVect*)]+0xb89): > undefined > reference to `std::basic_ostream >& std::endl > >(std::basic_ostream >&)' > OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode > moab::EigenDecomp(moab::Matrix3 const&, double*, moab::CartVect*)]+0xb91): > undefined > reference to `std::basic_ostream >::operator<<(std::basic___ostream std::char_traits >& (*)(std::basic_ostream >&))' > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o):(.eh_frame+__0x22f): undefined reference to > `__gxx_personality_v0' > collect2: ld returned 1 exit status > make: *** [nek5000] Error 1 > > Thanks, > Ami > > > _________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.__gov > https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > > > > -- > ==============================__==============================__==== > "You will keep in perfect peace him whose mind is > steadfast, because he trusts in you." Isaiah 26:3 > > Tim Tautges Argonne National Laboratory > (tautges at mcs.anl.gov ) (telecommuting from UW-Madison) > phone (gvoice): (608) 354-1459 1500 Engineering Dr. > fax: (608) 263-4499 Madison, WI 53706 > > _________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.__gov > https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -- ================================================================ "You will keep in perfect peace him whose mind is steadfast, because he trusts in you." Isaiah 26:3 Tim Tautges Argonne National Laboratory (tautges at mcs.anl.gov) (telecommuting from UW-Madison) phone (gvoice): (608) 354-1459 1500 Engineering Dr. fax: (608) 263-4499 Madison, WI 53706 From nek5000-users at lists.mcs.anl.gov Wed Sep 11 11:20:38 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Sep 2013 12:20:38 -0400 Subject: [Nek5000-users] Running MOAB example In-Reply-To: References: Message-ID: Yes , I am using gnu, and whwen I add USR_LFLAGS="-lmpi_cxx -lstdc++, I get this, makenek - automatic build tool for Nek5000 generating makefile ... mpif77 -c -O2 -fdefault-real-8 -x f77-cpp-input -fcray-pointer -DMOAB -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG -I/home/amirreza/nek5_svn/amirreza_test/examples/moab -I/home/amirreza/nek5_svn/trunk/nek -I./ /home/amirreza/nek5_svn/amirreza_test/examples/moab/pipe.f -I/home/amirreza/nek5_svn/trunk/nek/3rd_party -I/home/amirreza/Amirreza/moab-4.6.0/gcc/include -o obj/pipe.o mpif77 -o nek5000 obj/pipe.o obj/drive.o obj/drive1.o obj/drive2.o obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o obj/hsmg.o obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o obj/byte.o obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o obj/imeshutil.o obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o obj/jl_findpts_el_2.o obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o -L/home/amirreza/Amirreza/netcdf-4.1.3/gcc/lib -L/home/amirreza/Amirreza/zlib-1.2.5/gcc/lib -L/home/amirreza/Amirreza/szip-2.1/gcc/lib -L/home/amirreza/Amirreza/hdf5-1.8.11/lib -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib -liMesh -lMOAB -lnetcdf -lhdf5 -lsz -lm -lmpi_cxx -lstdc++ obj/moab.o: In function `nekmoab_intbc_': moab.f:(.text+0xe9d): undefined reference to `imesh_freememory_' moab.f:(.text+0xece): undefined reference to `imesh_freememory_' moab.f:(.text+0xee4): undefined reference to `imesh_freememory_' moab.f:(.text+0xf05): undefined reference to `imesh_freememory_' obj/moab.o: In function `nekmoab_bc_': moab.f:(.text+0x1306): undefined reference to `imesh_freememory_' collect2: ld returned 1 exit status make: *** [nek5000] Error 1 Thanks, Ami On Wed, Sep 11, 2013 at 12:05 PM, wrote: > It depends which compiler you're using. Are you using gnu? > > Please send complete compile output. > > - tim > > > On 09/11/2013 10:11 AM, nek5000-users at lists.mcs.anl.**govwrote: > >> Thanks for your answer, to make sure I have added libraries to makenek >> ''USR_LFLAGS="-lmpi_cxx -lstdc++" which I'm >> getting same error,so you mean I need to add appropriate fortran library >> to USR_LFLAGS? >> >> Thanks, >> Ami >> >> >> On Wed, Sep 11, 2013 at 10:47 AM, > nek5000-users at lists.**mcs.anl.gov >> >> wrote: >> >> Hi Ami, >> That's the C++ runtime. You have two options: >> 1. Link with the C++ compiler; in this case, you'll have to >> explicitly add the fortran runtime libraries to the link >> statement, which is most easily done by adding it to USR_LFLAGS in >> makenek. Compiler documents often tell you which >> libraries implement the fortran runtime, usually in a section about >> inter-language linking. >> >> 2. Add the C++ std libs to USR_LFLAGS. The trunk/nek/makenek file >> has a few examples of this method for >> gnu/intel/pgi. Sometimes, like on BG/x, it can be difficult to >> figure out what all comprises the C++ runtime, which >> is why I list 1. above. >> >> - tim >> >> >> On 09/11/2013 09:31 AM, nek5000-users at lists.mcs.anl.__**gov > nek5000-users at lists.**mcs.anl.gov > >> wrote: >> >> Hello Neks, >> >> I am trying to run MOAB example with nek5000, but all the time >> which I am running, it gives me set of undefined >> reference error. I put an error with last part of my ./makenek >> pipe log below. >> What is wrong with my work? >> >> IODebugTrack.cpp:(.text+0xb74)**__: undefined reference to >> `std::basic_ostream >& >> >> std::operator<< >> >(std::basic_ostream >&, char const*)' >> IODebugTrack.cpp:(.text+0xb7f)**__: undefined reference to >> `std::basic_ostream >> >::operator<<(unsigned long)' >> IODebugTrack.cpp:(.text+0xb8c)**__: undefined reference to >> `std::basic_ostream >& >> >> std::operator<< >> >(std::basic_ostream >&, char const*)' >> IODebugTrack.cpp:(.text+0xb97)**__: undefined reference to >> `std::basic_ostream >> >::operator<<(unsigned long)' >> IODebugTrack.cpp:(.text+0xbd3)**__: undefined reference to >> `std::basic_ostream >& >> >> std::operator<< >> >(std::basic_ostream >&, char const*)' >> IODebugTrack.cpp:(.text+0xbde)**__: undefined reference to >> `std::basic_ostream >> >::operator<<(unsigned long)' >> IODebugTrack.cpp:(.text+0xbeb)**__: undefined reference to >> `std::basic_ostream >& >> >> std::operator<< >> >(std::basic_ostream >&, char const*)' >> IODebugTrack.cpp:(.text+0xbf6)**__: undefined reference to >> `std::basic_ostream >> >::operator<<(unsigned long)' >> IODebugTrack.cpp:(.text+0xc03)**__: undefined reference to >> `std::basic_ostream >& >> >> std::operator<< >> >(std::basic_ostream >&, char const*)' >> IODebugTrack.cpp:(.text+0xc0e)**__: undefined reference to >> `std::basic_ostream >> >::operator<<(unsigned long)' >> IODebugTrack.cpp:(.text+0xc1b)**__: undefined reference to >> `std::basic_ostream >& >> >> std::operator<< >> >(std::basic_ostream >&, char const*)' >> IODebugTrack.cpp:(.text+0xc26)**__: undefined reference to >> `std::basic_ostream >> >::operator<<(unsigned long)' >> IODebugTrack.cpp:(.text+0xc33)**__: undefined reference to >> `std::basic_ostream >& >> >> std::operator<< >> >(std::basic_ostream >&, char const*)' >> IODebugTrack.cpp:(.text+0xc38)**__: undefined reference to >> `std::basic_ostream >& >> >> std::endl >(std::basic_ostream> std::char_traits >&)' >> IODebugTrack.cpp:(.text+0xc40)**__: undefined reference to >> `std::basic_ostream >> >::operator<<(std::basic___**ostream> std::char_traits >& (*)(std::basic_ostream> std::char_traits >&))' >> IODebugTrack.cpp:(.text+0xc50)**__: undefined reference to >> `std::basic_ostream >> >::flush()' >> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**IODebugTrack.o): >> In function >> `moab::IODebugTrack::all___**reduce()': >> IODebugTrack.cpp:(.text+0xd08)**__: undefined reference to >> `MPI_Comm_size' >> IODebugTrack.cpp:(.text+0xdfe)**__: undefined reference to >> `MPI_Gather' >> IODebugTrack.cpp:(.text+__**0x1080): undefined reference to >> `MPI_Gatherv' >> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**IODebugTrack.o): >> In function >> `__static_initialization_and__**_destruction_0(int, int)': >> IODebugTrack.cpp:(.text+__**0x1221): undefined reference to >> `std::ios_base::Init::Init()' >> IODebugTrack.cpp:(.text+__**0x1226): undefined reference to >> `std::ios_base::Init::~Init()' >> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**IODebugTrack.o): >> In function >> `std::list> std::allocator >> >::_M_insert(std::_List___**iterator, >> moab::IODebugTrack::DRange const&)': >> IODebugTrack.cpp:(.text.___**ZNSt4listIN4moab12IODebugTrack** >> __6DRangeESaIS2_EE9_M___**insertESt14_List_iteratorIS2__** >> _ERKS2_[std::list> std::allocator >> >::_M_insert(std::_List___**iterator, >> >> moab::IODebugTrack::DRange const&)]+0x3a): undefined reference to >> `std::__detail::_List_node___**base::_M_hook(std::__detail::_** >> __List_node_base*)' >> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**IODebugTrack.o): >> In function >> `__gnu_cxx::new_allocator> IODebugTrack::DRange> >> >::deallocate(std::_List_node<**__moab::IODebugTrack::DRange>** >> *, unsigned long)': >> IODebugTrack.cpp:(.text._ZN9__**__gnu_cxx13new_allocatorISt10_** >> __List___**nodeIN4moab12IODebugTrack6DRan**__geEEE10deallocateEPS5_m[__** >> gnu___cxx::new_allocator> IODebugTrack::__DRange> >> >::deallocate(std::_List_node<**__moab::IODebugTrack::DRange>** >> *, unsigned long)]+0x1c): undefined reference to >> `operator >> delete(void*)' >> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**IODebugTrack.o): >> In function >> `__gnu_cxx::new_allocator<__**moab::IODebugTrack::DRange>::_**_allocate(unsigned >> long, void const*)': >> IODebugTrack.cpp:(.text._ZN9__**__gnu_cxx13new___** >> allocatorIN4moab12IODebugTrack**__6DRangeEE8allocateEmPKv[__** >> gnu___cxx::new_allocator::__** >> allocate(unsigned >> >> long, void const*)]+0x2c): undefined reference to >> `std::__throw_bad_alloc()' >> IODebugTrack.cpp:(.text._ZN9__**__gnu_cxx13new___** >> allocatorIN4moab12IODebugTrack**__6DRangeEE8allocateEmPKv[__** >> gnu___cxx::new_allocator::__** >> allocate(unsigned >> >> long, void const*)]+0x45): undefined reference to `operator >> new(unsigned long)' >> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**IODebugTrack.o): >> In function >> `__gnu_cxx::new_allocator<__**moab::IODebugTrack::DRange>::_** >> _deallocate(moab::**IODebugTrack:__:DRange*, unsigned >> long)': >> IODebugTrack.cpp:(.text._ZN9__**__gnu_cxx13new___** >> allocatorIN4moab12IODebugTrack**__6DRangeEE10deallocateEPS3_m[** >> ____gnu_cxx::new_allocator<**moab::__IODebugTrack::DRange>:** >> :__deallocate(moab::**IODebugTrack:__:DRange*, >> >> unsigned long)]+0x1c): undefined reference to `operator >> delete(void*)' >> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**IODebugTrack.o): >> In function >> `__gnu_cxx::new_allocator >> >::allocate(unsigned long, void const*)': >> IODebugTrack.cpp:(.text._ZN9__**__gnu_cxx13new_allocatorISt10_** >> __List___**nodeIN4moab12IODebugTrack6DRan**__geEEE8allocateEmPKv[__gnu_** >> cxx:__:new_allocator >> >> >::allocate(unsigned long, void const*)]+0x2c): undefined >> reference to `std::__throw_bad_alloc()' >> IODebugTrack.cpp:(.text._ZN9__**__gnu_cxx13new_allocatorISt10_** >> __List___**nodeIN4moab12IODebugTrack6DRan**__geEEE8allocateEmPKv[__gnu_** >> cxx:__:new_allocator >> >> >::allocate(unsigned long, void const*)]+0x46): undefined >> reference to `operator new(unsigned long)' >> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__** >> IODebugTrack.o):(.eh_frame+__**0x24b): undefined reference to >> `__gxx_personality_v0' >> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**OrientedBox.o): >> In function >> `moab::operator<<(std::basic__**_ostream> std::char_traits >&, moab::OrientedBox const&)': >> >> OrientedBox.cpp:(.text+0x97): undefined reference to >> `std::basic_ostream >& >> std::operator<< >> >(std::basic_ostream> std::char_traits >&, char const*)' >> OrientedBox.cpp:(.text+0xaf): undefined reference to >> `std::basic_ostream >& >> std::operator<< >> >(std::basic_ostream> std::char_traits >&, char const*)' >> OrientedBox.cpp:(.text+0xbc): undefined reference to >> `std::basic_ostream >> >::operator<<(double)' >> OrientedBox.cpp:(.text+0xc9): undefined reference to >> `std::basic_ostream >& >> std::operator<< >> >(std::basic_ostream> std::char_traits >&, char const*)' >> OrientedBox.cpp:(.text+0xe1): undefined reference to >> `std::basic_ostream >& >> std::operator<< >> >(std::basic_ostream> std::char_traits >&, char const*)' >> OrientedBox.cpp:(.text+0xee): undefined reference to >> `std::basic_ostream >> >::operator<<(double)' >> OrientedBox.cpp:(.text+0xfb): undefined reference to >> `std::basic_ostream >& >> std::operator<< >> >(std::basic_ostream> std::char_traits >&, char const*)' >> OrientedBox.cpp:(.text+0x113): undefined reference to >> `std::basic_ostream >& >> std::operator<< >> >(std::basic_ostream >&, char const*)' >> OrientedBox.cpp:(.text+0x120): undefined reference to >> `std::basic_ostream >> >::operator<<(double)' >> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**OrientedBox.o): >> In function >> `__static_initialization_and__**_destruction_0(int, int)': >> OrientedBox.cpp:(.text+0x3aaf)**__: undefined reference to >> `std::ios_base::Init::Init()' >> OrientedBox.cpp:(.text+0x3ab4)**__: undefined reference to >> `std::ios_base::Init::~Init()' >> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**OrientedBox.o): >> In function `moab::ErrorCode >> moab::EigenDecomp> moab::CartVect>(moab::Matrix3 const&, double*, moab::CartVect*)': >> OrientedBox.cpp:(.text.___**ZN4moab11EigenDecompINS___** >> 7Matrix3ENS_8CartVectEEENS___**9ErrorCodeERKT_PdPT0_[moab::__**ErrorCode >> moab::EigenDecomp> moab::CartVect>(moab::Matrix3 const&, double*, moab::CartVect*)]+0xb7f): >> >> undefined >> reference to `std::cerr' >> OrientedBox.cpp:(.text.___**ZN4moab11EigenDecompINS___** >> 7Matrix3ENS_8CartVectEEENS___**9ErrorCodeERKT_PdPT0_[moab::__**ErrorCode >> moab::EigenDecomp> moab::CartVect>(moab::Matrix3 const&, double*, moab::CartVect*)]+0xb84): >> >> undefined >> reference to `std::basic_ostream >& >> std::operator<< >> >(std::basic_ostream >&, char >> const*)' >> OrientedBox.cpp:(.text.___**ZN4moab11EigenDecompINS___** >> 7Matrix3ENS_8CartVectEEENS___**9ErrorCodeERKT_PdPT0_[moab::__**ErrorCode >> moab::EigenDecomp> moab::CartVect>(moab::Matrix3 const&, double*, moab::CartVect*)]+0xb89): >> >> undefined >> reference to `std::basic_ostream >& >> std::endl >> >(std::basic_ostream >&)' >> OrientedBox.cpp:(.text.___**ZN4moab11EigenDecompINS___** >> 7Matrix3ENS_8CartVectEEENS___**9ErrorCodeERKT_PdPT0_[moab::__**ErrorCode >> moab::EigenDecomp> moab::CartVect>(moab::Matrix3 const&, double*, moab::CartVect*)]+0xb91): >> undefined >> reference to `std::basic_ostream >> >::operator<<(std::basic___**ostream> >> std::char_traits >& (*)(std::basic_ostream> std::char_traits >&))' >> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__** >> OrientedBox.o):(.eh_frame+__**0x22f): undefined reference to >> >> `__gxx_personality_v0' >> collect2: ld returned 1 exit status >> make: *** [nek5000] Error 1 >> >> Thanks, >> Ami >> >> >> ______________________________**___________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.__**gov > *mcs.anl.gov > >> https://lists.mcs.anl.gov/__**mailman/listinfo/nek5000-users >> >> **> >> >> >> -- >> ==============================**__============================** >> ==__==== >> >> "You will keep in perfect peace him whose mind is >> steadfast, because he trusts in you." Isaiah 26:3 >> >> Tim Tautges Argonne National Laboratory >> (tautges at mcs.anl.gov ) >> (telecommuting from UW-Madison) >> phone (gvoice): (608) 354-1459 >> 1500 Engineering Dr. >> fax: (608) 263-4499 >> Madison, WI 53706 >> >> ______________________________**___________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.__**gov > mcs.anl.gov > >> https://lists.mcs.anl.gov/__**mailman/listinfo/nek5000-users< >> https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users >> **> >> >> >> >> >> >> ______________________________**_________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.**gov >> https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users >> >> > -- > ==============================**==============================**==== > "You will keep in perfect peace him whose mind is > steadfast, because he trusts in you." Isaiah 26:3 > > Tim Tautges Argonne National Laboratory > (tautges at mcs.anl.gov) (telecommuting from UW-Madison) > phone (gvoice): (608) 354-1459 1500 Engineering Dr. > fax: (608) 263-4499 Madison, WI 53706 > > ______________________________**_________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.**gov > https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Sep 11 11:33:15 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Sep 2013 11:33:15 -0500 Subject: [Nek5000-users] Running MOAB example In-Reply-To: References: Message-ID: The linker error is because of your version mismatch. You need to update your moab to the latest version. I see you are using v4.6 now. You should be able to use the dev version from https://bitbucket.org/fathomteam/moab with git or download the newer patch from https://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB. Tim, can we create a new patched version of the release for download. I spoke to Rajeev about this some time back but we need to decide what fixes to backport. Vijay On Wed, Sep 11, 2013 at 11:20 AM, wrote: > > Yes , I am using gnu, and whwen I add USR_LFLAGS="-lmpi_cxx -lstdc++, > I get this, > makenek - automatic build tool for Nek5000 > generating makefile ... > mpif77 -c -O2 -fdefault-real-8 -x f77-cpp-input -fcray-pointer -DMOAB > -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG > -I/home/amirreza/nek5_svn/amirreza_test/examples/moab > -I/home/amirreza/nek5_svn/trunk/nek -I./ > /home/amirreza/nek5_svn/amirreza_test/examples/moab/pipe.f > -I/home/amirreza/nek5_svn/trunk/nek/3rd_party > -I/home/amirreza/Amirreza/moab-4.6.0/gcc/include -o obj/pipe.o > mpif77 -o nek5000 obj/pipe.o obj/drive.o obj/drive1.o obj/drive2.o > obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o > obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o > obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o > obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o > obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o > obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o > obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o obj/hsmg.o > obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o > obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o obj/byte.o > obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o > obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o > obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o > obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o obj/imeshutil.o > obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o > obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o > obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o > obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o > obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o obj/jl_findpts_el_2.o > obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o > -L/home/amirreza/Amirreza/netcdf-4.1.3/gcc/lib > -L/home/amirreza/Amirreza/zlib-1.2.5/gcc/lib > -L/home/amirreza/Amirreza/szip-2.1/gcc/lib > -L/home/amirreza/Amirreza/hdf5-1.8.11/lib > -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib > -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib -liMesh -lMOAB -lnetcdf -lhdf5 > -lsz -lm -lmpi_cxx -lstdc++ > obj/moab.o: In function `nekmoab_intbc_': > moab.f:(.text+0xe9d): undefined reference to `imesh_freememory_' > moab.f:(.text+0xece): undefined reference to `imesh_freememory_' > moab.f:(.text+0xee4): undefined reference to `imesh_freememory_' > moab.f:(.text+0xf05): undefined reference to `imesh_freememory_' > obj/moab.o: In function `nekmoab_bc_': > moab.f:(.text+0x1306): undefined reference to `imesh_freememory_' > > collect2: ld returned 1 exit status > make: *** [nek5000] Error 1 > > Thanks, > Ami > > > On Wed, Sep 11, 2013 at 12:05 PM, wrote: >> >> It depends which compiler you're using. Are you using gnu? >> >> Please send complete compile output. >> >> - tim >> >> >> On 09/11/2013 10:11 AM, nek5000-users at lists.mcs.anl.gov wrote: >>> >>> Thanks for your answer, to make sure I have added libraries to makenek >>> ''USR_LFLAGS="-lmpi_cxx -lstdc++" which I'm >>> getting same error,so you mean I need to add appropriate fortran library >>> to USR_LFLAGS? >>> >>> Thanks, >>> Ami >>> >>> >>> On Wed, Sep 11, 2013 at 10:47 AM, >> > wrote: >>> >>> Hi Ami, >>> That's the C++ runtime. You have two options: >>> 1. Link with the C++ compiler; in this case, you'll have to >>> explicitly add the fortran runtime libraries to the link >>> statement, which is most easily done by adding it to USR_LFLAGS in >>> makenek. Compiler documents often tell you which >>> libraries implement the fortran runtime, usually in a section about >>> inter-language linking. >>> >>> 2. Add the C++ std libs to USR_LFLAGS. The trunk/nek/makenek file >>> has a few examples of this method for >>> gnu/intel/pgi. Sometimes, like on BG/x, it can be difficult to >>> figure out what all comprises the C++ runtime, which >>> is why I list 1. above. >>> >>> - tim >>> >>> >>> On 09/11/2013 09:31 AM, nek5000-users at lists.mcs.anl.__gov >>> wrote: >>> >>> Hello Neks, >>> >>> I am trying to run MOAB example with nek5000, but all the time >>> which I am running, it gives me set of undefined >>> reference error. I put an error with last part of my ./makenek >>> pipe log below. >>> What is wrong with my work? >>> >>> IODebugTrack.cpp:(.text+0xb74)__: undefined reference to >>> `std::basic_ostream >& >>> >>> std::operator<< >>> >(std::basic_ostream >&, char const*)' >>> IODebugTrack.cpp:(.text+0xb7f)__: undefined reference to >>> `std::basic_ostream >>> >::operator<<(unsigned long)' >>> IODebugTrack.cpp:(.text+0xb8c)__: undefined reference to >>> `std::basic_ostream >& >>> >>> std::operator<< >>> >(std::basic_ostream >&, char const*)' >>> IODebugTrack.cpp:(.text+0xb97)__: undefined reference to >>> `std::basic_ostream >>> >::operator<<(unsigned long)' >>> IODebugTrack.cpp:(.text+0xbd3)__: undefined reference to >>> `std::basic_ostream >& >>> >>> std::operator<< >>> >(std::basic_ostream >&, char const*)' >>> IODebugTrack.cpp:(.text+0xbde)__: undefined reference to >>> `std::basic_ostream >>> >::operator<<(unsigned long)' >>> IODebugTrack.cpp:(.text+0xbeb)__: undefined reference to >>> `std::basic_ostream >& >>> >>> std::operator<< >>> >(std::basic_ostream >&, char const*)' >>> IODebugTrack.cpp:(.text+0xbf6)__: undefined reference to >>> `std::basic_ostream >>> >::operator<<(unsigned long)' >>> IODebugTrack.cpp:(.text+0xc03)__: undefined reference to >>> `std::basic_ostream >& >>> >>> std::operator<< >>> >(std::basic_ostream >&, char const*)' >>> IODebugTrack.cpp:(.text+0xc0e)__: undefined reference to >>> `std::basic_ostream >>> >::operator<<(unsigned long)' >>> IODebugTrack.cpp:(.text+0xc1b)__: undefined reference to >>> `std::basic_ostream >& >>> >>> std::operator<< >>> >(std::basic_ostream >&, char const*)' >>> IODebugTrack.cpp:(.text+0xc26)__: undefined reference to >>> `std::basic_ostream >>> >::operator<<(unsigned long)' >>> IODebugTrack.cpp:(.text+0xc33)__: undefined reference to >>> `std::basic_ostream >& >>> >>> std::operator<< >>> >(std::basic_ostream >&, char const*)' >>> IODebugTrack.cpp:(.text+0xc38)__: undefined reference to >>> `std::basic_ostream >& >>> >>> std::endl >(std::basic_ostream>> std::char_traits >&)' >>> IODebugTrack.cpp:(.text+0xc40)__: undefined reference to >>> `std::basic_ostream >>> >::operator<<(std::basic___ostream >>> >& (*)(std::basic_ostream>> std::char_traits >&))' >>> IODebugTrack.cpp:(.text+0xc50)__: undefined reference to >>> `std::basic_ostream >>> >::flush()' >>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> function >>> `moab::IODebugTrack::all___reduce()': >>> IODebugTrack.cpp:(.text+0xd08)__: undefined reference to >>> `MPI_Comm_size' >>> IODebugTrack.cpp:(.text+0xdfe)__: undefined reference to >>> `MPI_Gather' >>> IODebugTrack.cpp:(.text+__0x1080): undefined reference to >>> `MPI_Gatherv' >>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> function >>> `__static_initialization_and___destruction_0(int, int)': >>> IODebugTrack.cpp:(.text+__0x1221): undefined reference to >>> `std::ios_base::Init::Init()' >>> IODebugTrack.cpp:(.text+__0x1226): undefined reference to >>> `std::ios_base::Init::~Init()' >>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> function >>> `std::list>> std::allocator >>> >::_M_insert(std::_List___iterator, >>> moab::IODebugTrack::DRange const&)': >>> >>> IODebugTrack.cpp:(.text.___ZNSt4listIN4moab12IODebugTrack__6DRangeESaIS2_EE9_M___insertESt14_List_iteratorIS2___ERKS2_[std::list>> std::allocator >>> >::_M_insert(std::_List___iterator, >>> >>> moab::IODebugTrack::DRange const&)]+0x3a): undefined reference to >>> >>> `std::__detail::_List_node___base::_M_hook(std::__detail::___List_node_base*)' >>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> function >>> >>> `__gnu_cxx::new_allocator >>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, >>> unsigned long)': >>> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE10deallocateEPS5_m[__gnu___cxx::new_allocator >>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, >>> unsigned long)]+0x1c): undefined reference to >>> `operator >>> delete(void*)' >>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> function >>> >>> `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__allocate(unsigned >>> long, void const*)': >>> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned >>> >>> long, void const*)]+0x2c): undefined reference to >>> `std::__throw_bad_alloc()' >>> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned >>> >>> long, void const*)]+0x45): undefined reference to `operator >>> new(unsigned long)' >>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> function >>> >>> `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__deallocate(moab::IODebugTrack:__:DRange*, >>> unsigned >>> long)': >>> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE10deallocateEPS3_m[____gnu_cxx::new_allocator::__deallocate(moab::IODebugTrack:__:DRange*, >>> >>> unsigned long)]+0x1c): undefined reference to `operator >>> delete(void*)' >>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> function >>> >>> `__gnu_cxx::new_allocator >>> >::allocate(unsigned long, void const*)': >>> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator >>> >>> >::allocate(unsigned long, void const*)]+0x2c): undefined >>> reference to `std::__throw_bad_alloc()' >>> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator >>> >>> >::allocate(unsigned long, void const*)]+0x46): undefined >>> reference to `operator new(unsigned long)' >>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o):(.eh_frame+__0x24b): >>> undefined reference to >>> `__gxx_personality_v0' >>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In >>> function >>> `moab::operator<<(std::basic___ostream>> std::char_traits >&, moab::OrientedBox const&)': >>> >>> OrientedBox.cpp:(.text+0x97): undefined reference to >>> `std::basic_ostream >& >>> std::operator<< >>> >(std::basic_ostream>> std::char_traits >&, char const*)' >>> OrientedBox.cpp:(.text+0xaf): undefined reference to >>> `std::basic_ostream >& >>> std::operator<< >>> >(std::basic_ostream>> std::char_traits >&, char const*)' >>> OrientedBox.cpp:(.text+0xbc): undefined reference to >>> `std::basic_ostream >>> >::operator<<(double)' >>> OrientedBox.cpp:(.text+0xc9): undefined reference to >>> `std::basic_ostream >& >>> std::operator<< >>> >(std::basic_ostream>> std::char_traits >&, char const*)' >>> OrientedBox.cpp:(.text+0xe1): undefined reference to >>> `std::basic_ostream >& >>> std::operator<< >>> >(std::basic_ostream>> std::char_traits >&, char const*)' >>> OrientedBox.cpp:(.text+0xee): undefined reference to >>> `std::basic_ostream >>> >::operator<<(double)' >>> OrientedBox.cpp:(.text+0xfb): undefined reference to >>> `std::basic_ostream >& >>> std::operator<< >>> >(std::basic_ostream>> std::char_traits >&, char const*)' >>> OrientedBox.cpp:(.text+0x113): undefined reference to >>> `std::basic_ostream >& >>> std::operator<< >>> >(std::basic_ostream >&, char const*)' >>> OrientedBox.cpp:(.text+0x120): undefined reference to >>> `std::basic_ostream >>> >::operator<<(double)' >>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In >>> function >>> `__static_initialization_and___destruction_0(int, int)': >>> OrientedBox.cpp:(.text+0x3aaf)__: undefined reference to >>> `std::ios_base::Init::Init()' >>> OrientedBox.cpp:(.text+0x3ab4)__: undefined reference to >>> `std::ios_base::Init::~Init()' >>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In >>> function `moab::ErrorCode >>> moab::EigenDecomp(moab::Matrix3 >>> const&, double*, moab::CartVect*)': >>> >>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>> moab::EigenDecomp(moab::Matrix3 >>> const&, double*, moab::CartVect*)]+0xb7f): >>> >>> undefined >>> reference to `std::cerr' >>> >>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>> moab::EigenDecomp(moab::Matrix3 >>> const&, double*, moab::CartVect*)]+0xb84): >>> >>> undefined >>> reference to `std::basic_ostream >& >>> std::operator<< >>> >(std::basic_ostream >&, char >>> const*)' >>> >>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>> moab::EigenDecomp(moab::Matrix3 >>> const&, double*, moab::CartVect*)]+0xb89): >>> >>> undefined >>> reference to `std::basic_ostream >& >>> std::endl >>> >(std::basic_ostream >&)' >>> >>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>> moab::EigenDecomp(moab::Matrix3 >>> const&, double*, moab::CartVect*)]+0xb91): >>> undefined >>> reference to `std::basic_ostream >>> >::operator<<(std::basic___ostream>> >>> std::char_traits >& (*)(std::basic_ostream>> std::char_traits >&))' >>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o):(.eh_frame+__0x22f): >>> undefined reference to >>> >>> `__gxx_personality_v0' >>> collect2: ld returned 1 exit status >>> make: *** [nek5000] Error 1 >>> >>> Thanks, >>> Ami >>> >>> >>> _________________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.__gov >>> >>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >>> >>> >>> >>> -- >>> ==============================__==============================__==== >>> >>> "You will keep in perfect peace him whose mind is >>> steadfast, because he trusts in you." Isaiah 26:3 >>> >>> Tim Tautges Argonne National Laboratory >>> (tautges at mcs.anl.gov ) >>> (telecommuting from UW-Madison) >>> phone (gvoice): (608) 354-1459 1500 >>> Engineering Dr. >>> fax: (608) 263-4499 >>> Madison, WI 53706 >>> >>> _________________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.__gov >>> >>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> >> -- >> ================================================================ >> "You will keep in perfect peace him whose mind is >> steadfast, because he trusts in you." Isaiah 26:3 >> >> Tim Tautges Argonne National Laboratory >> (tautges at mcs.anl.gov) (telecommuting from UW-Madison) >> phone (gvoice): (608) 354-1459 1500 Engineering Dr. >> fax: (608) 263-4499 Madison, WI 53706 >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Wed Sep 11 11:36:58 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Sep 2013 11:36:58 -0500 Subject: [Nek5000-users] Running MOAB example In-Reply-To: References: Message-ID: Aha, good catch. Iulian, could you backport the imesh_freememory function? Thanks. - tim On 09/11/2013 11:33 AM, Vijay S. Mahadevan wrote: > The linker error is because of your version mismatch. You need to > update your moab to the latest version. I see you are using v4.6 now. > You should be able to use the dev version from > https://bitbucket.org/fathomteam/moab with git or download the newer > patch from https://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB. > > Tim, can we create a new patched version of the release for download. > I spoke to Rajeev about this some time back but we need to decide what > fixes to backport. > > Vijay > > On Wed, Sep 11, 2013 at 11:20 AM, wrote: >> >> Yes , I am using gnu, and whwen I add USR_LFLAGS="-lmpi_cxx -lstdc++, >> I get this, >> makenek - automatic build tool for Nek5000 >> generating makefile ... >> mpif77 -c -O2 -fdefault-real-8 -x f77-cpp-input -fcray-pointer -DMOAB >> -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG >> -I/home/amirreza/nek5_svn/amirreza_test/examples/moab >> -I/home/amirreza/nek5_svn/trunk/nek -I./ >> /home/amirreza/nek5_svn/amirreza_test/examples/moab/pipe.f >> -I/home/amirreza/nek5_svn/trunk/nek/3rd_party >> -I/home/amirreza/Amirreza/moab-4.6.0/gcc/include -o obj/pipe.o >> mpif77 -o nek5000 obj/pipe.o obj/drive.o obj/drive1.o obj/drive2.o >> obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o >> obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o >> obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o >> obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o >> obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o >> obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o >> obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o obj/hsmg.o >> obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o >> obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o obj/byte.o >> obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o >> obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o >> obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o >> obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o obj/imeshutil.o >> obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o >> obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o >> obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o >> obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o >> obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o obj/jl_findpts_el_2.o >> obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o >> -L/home/amirreza/Amirreza/netcdf-4.1.3/gcc/lib >> -L/home/amirreza/Amirreza/zlib-1.2.5/gcc/lib >> -L/home/amirreza/Amirreza/szip-2.1/gcc/lib >> -L/home/amirreza/Amirreza/hdf5-1.8.11/lib >> -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib >> -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib -liMesh -lMOAB -lnetcdf -lhdf5 >> -lsz -lm -lmpi_cxx -lstdc++ >> obj/moab.o: In function `nekmoab_intbc_': >> moab.f:(.text+0xe9d): undefined reference to `imesh_freememory_' >> moab.f:(.text+0xece): undefined reference to `imesh_freememory_' >> moab.f:(.text+0xee4): undefined reference to `imesh_freememory_' >> moab.f:(.text+0xf05): undefined reference to `imesh_freememory_' >> obj/moab.o: In function `nekmoab_bc_': >> moab.f:(.text+0x1306): undefined reference to `imesh_freememory_' >> >> collect2: ld returned 1 exit status >> make: *** [nek5000] Error 1 >> >> Thanks, >> Ami >> >> >> On Wed, Sep 11, 2013 at 12:05 PM, wrote: >>> >>> It depends which compiler you're using. Are you using gnu? >>> >>> Please send complete compile output. >>> >>> - tim >>> >>> >>> On 09/11/2013 10:11 AM, nek5000-users at lists.mcs.anl.gov wrote: >>>> >>>> Thanks for your answer, to make sure I have added libraries to makenek >>>> ''USR_LFLAGS="-lmpi_cxx -lstdc++" which I'm >>>> getting same error,so you mean I need to add appropriate fortran library >>>> to USR_LFLAGS? >>>> >>>> Thanks, >>>> Ami >>>> >>>> >>>> On Wed, Sep 11, 2013 at 10:47 AM, >>> > wrote: >>>> >>>> Hi Ami, >>>> That's the C++ runtime. You have two options: >>>> 1. Link with the C++ compiler; in this case, you'll have to >>>> explicitly add the fortran runtime libraries to the link >>>> statement, which is most easily done by adding it to USR_LFLAGS in >>>> makenek. Compiler documents often tell you which >>>> libraries implement the fortran runtime, usually in a section about >>>> inter-language linking. >>>> >>>> 2. Add the C++ std libs to USR_LFLAGS. The trunk/nek/makenek file >>>> has a few examples of this method for >>>> gnu/intel/pgi. Sometimes, like on BG/x, it can be difficult to >>>> figure out what all comprises the C++ runtime, which >>>> is why I list 1. above. >>>> >>>> - tim >>>> >>>> >>>> On 09/11/2013 09:31 AM, nek5000-users at lists.mcs.anl.__gov >>>> wrote: >>>> >>>> Hello Neks, >>>> >>>> I am trying to run MOAB example with nek5000, but all the time >>>> which I am running, it gives me set of undefined >>>> reference error. I put an error with last part of my ./makenek >>>> pipe log below. >>>> What is wrong with my work? >>>> >>>> IODebugTrack.cpp:(.text+0xb74)__: undefined reference to >>>> `std::basic_ostream >& >>>> >>>> std::operator<< >>>>> (std::basic_ostream >&, char const*)' >>>> IODebugTrack.cpp:(.text+0xb7f)__: undefined reference to >>>> `std::basic_ostream >>>> >::operator<<(unsigned long)' >>>> IODebugTrack.cpp:(.text+0xb8c)__: undefined reference to >>>> `std::basic_ostream >& >>>> >>>> std::operator<< >>>>> (std::basic_ostream >&, char const*)' >>>> IODebugTrack.cpp:(.text+0xb97)__: undefined reference to >>>> `std::basic_ostream >>>> >::operator<<(unsigned long)' >>>> IODebugTrack.cpp:(.text+0xbd3)__: undefined reference to >>>> `std::basic_ostream >& >>>> >>>> std::operator<< >>>>> (std::basic_ostream >&, char const*)' >>>> IODebugTrack.cpp:(.text+0xbde)__: undefined reference to >>>> `std::basic_ostream >>>> >::operator<<(unsigned long)' >>>> IODebugTrack.cpp:(.text+0xbeb)__: undefined reference to >>>> `std::basic_ostream >& >>>> >>>> std::operator<< >>>>> (std::basic_ostream >&, char const*)' >>>> IODebugTrack.cpp:(.text+0xbf6)__: undefined reference to >>>> `std::basic_ostream >>>> >::operator<<(unsigned long)' >>>> IODebugTrack.cpp:(.text+0xc03)__: undefined reference to >>>> `std::basic_ostream >& >>>> >>>> std::operator<< >>>>> (std::basic_ostream >&, char const*)' >>>> IODebugTrack.cpp:(.text+0xc0e)__: undefined reference to >>>> `std::basic_ostream >>>> >::operator<<(unsigned long)' >>>> IODebugTrack.cpp:(.text+0xc1b)__: undefined reference to >>>> `std::basic_ostream >& >>>> >>>> std::operator<< >>>>> (std::basic_ostream >&, char const*)' >>>> IODebugTrack.cpp:(.text+0xc26)__: undefined reference to >>>> `std::basic_ostream >>>> >::operator<<(unsigned long)' >>>> IODebugTrack.cpp:(.text+0xc33)__: undefined reference to >>>> `std::basic_ostream >& >>>> >>>> std::operator<< >>>>> (std::basic_ostream >&, char const*)' >>>> IODebugTrack.cpp:(.text+0xc38)__: undefined reference to >>>> `std::basic_ostream >& >>>> >>>> std::endl >(std::basic_ostream>>> std::char_traits >&)' >>>> IODebugTrack.cpp:(.text+0xc40)__: undefined reference to >>>> `std::basic_ostream >>>> >::operator<<(std::basic___ostream >>>>> & (*)(std::basic_ostream>>> std::char_traits >&))' >>>> IODebugTrack.cpp:(.text+0xc50)__: undefined reference to >>>> `std::basic_ostream >>>> >::flush()' >>>> >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>>> function >>>> `moab::IODebugTrack::all___reduce()': >>>> IODebugTrack.cpp:(.text+0xd08)__: undefined reference to >>>> `MPI_Comm_size' >>>> IODebugTrack.cpp:(.text+0xdfe)__: undefined reference to >>>> `MPI_Gather' >>>> IODebugTrack.cpp:(.text+__0x1080): undefined reference to >>>> `MPI_Gatherv' >>>> >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>>> function >>>> `__static_initialization_and___destruction_0(int, int)': >>>> IODebugTrack.cpp:(.text+__0x1221): undefined reference to >>>> `std::ios_base::Init::Init()' >>>> IODebugTrack.cpp:(.text+__0x1226): undefined reference to >>>> `std::ios_base::Init::~Init()' >>>> >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>>> function >>>> `std::list>>> std::allocator >>>>> ::_M_insert(std::_List___iterator, >>>> moab::IODebugTrack::DRange const&)': >>>> >>>> IODebugTrack.cpp:(.text.___ZNSt4listIN4moab12IODebugTrack__6DRangeESaIS2_EE9_M___insertESt14_List_iteratorIS2___ERKS2_[std::list>>> std::allocator >>>>> ::_M_insert(std::_List___iterator, >>>> >>>> moab::IODebugTrack::DRange const&)]+0x3a): undefined reference to >>>> >>>> `std::__detail::_List_node___base::_M_hook(std::__detail::___List_node_base*)' >>>> >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>>> function >>>> >>>> `__gnu_cxx::new_allocator >>>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, >>>> unsigned long)': >>>> >>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE10deallocateEPS5_m[__gnu___cxx::new_allocator >>>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, >>>> unsigned long)]+0x1c): undefined reference to >>>> `operator >>>> delete(void*)' >>>> >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>>> function >>>> >>>> `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__allocate(unsigned >>>> long, void const*)': >>>> >>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned >>>> >>>> long, void const*)]+0x2c): undefined reference to >>>> `std::__throw_bad_alloc()' >>>> >>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned >>>> >>>> long, void const*)]+0x45): undefined reference to `operator >>>> new(unsigned long)' >>>> >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>>> function >>>> >>>> `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__deallocate(moab::IODebugTrack:__:DRange*, >>>> unsigned >>>> long)': >>>> >>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE10deallocateEPS3_m[____gnu_cxx::new_allocator::__deallocate(moab::IODebugTrack:__:DRange*, >>>> >>>> unsigned long)]+0x1c): undefined reference to `operator >>>> delete(void*)' >>>> >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>>> function >>>> >>>> `__gnu_cxx::new_allocator >>>>> ::allocate(unsigned long, void const*)': >>>> >>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator >>>> >>>> >::allocate(unsigned long, void const*)]+0x2c): undefined >>>> reference to `std::__throw_bad_alloc()' >>>> >>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator >>>> >>>> >::allocate(unsigned long, void const*)]+0x46): undefined >>>> reference to `operator new(unsigned long)' >>>> >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o):(.eh_frame+__0x24b): >>>> undefined reference to >>>> `__gxx_personality_v0' >>>> >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In >>>> function >>>> `moab::operator<<(std::basic___ostream>>> std::char_traits >&, moab::OrientedBox const&)': >>>> >>>> OrientedBox.cpp:(.text+0x97): undefined reference to >>>> `std::basic_ostream >& >>>> std::operator<< >>>> >(std::basic_ostream>>> std::char_traits >&, char const*)' >>>> OrientedBox.cpp:(.text+0xaf): undefined reference to >>>> `std::basic_ostream >& >>>> std::operator<< >>>> >(std::basic_ostream>>> std::char_traits >&, char const*)' >>>> OrientedBox.cpp:(.text+0xbc): undefined reference to >>>> `std::basic_ostream >>>> >::operator<<(double)' >>>> OrientedBox.cpp:(.text+0xc9): undefined reference to >>>> `std::basic_ostream >& >>>> std::operator<< >>>> >(std::basic_ostream>>> std::char_traits >&, char const*)' >>>> OrientedBox.cpp:(.text+0xe1): undefined reference to >>>> `std::basic_ostream >& >>>> std::operator<< >>>> >(std::basic_ostream>>> std::char_traits >&, char const*)' >>>> OrientedBox.cpp:(.text+0xee): undefined reference to >>>> `std::basic_ostream >>>> >::operator<<(double)' >>>> OrientedBox.cpp:(.text+0xfb): undefined reference to >>>> `std::basic_ostream >& >>>> std::operator<< >>>> >(std::basic_ostream>>> std::char_traits >&, char const*)' >>>> OrientedBox.cpp:(.text+0x113): undefined reference to >>>> `std::basic_ostream >& >>>> std::operator<< >>>>> (std::basic_ostream >&, char const*)' >>>> OrientedBox.cpp:(.text+0x120): undefined reference to >>>> `std::basic_ostream >>>> >::operator<<(double)' >>>> >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In >>>> function >>>> `__static_initialization_and___destruction_0(int, int)': >>>> OrientedBox.cpp:(.text+0x3aaf)__: undefined reference to >>>> `std::ios_base::Init::Init()' >>>> OrientedBox.cpp:(.text+0x3ab4)__: undefined reference to >>>> `std::ios_base::Init::~Init()' >>>> >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In >>>> function `moab::ErrorCode >>>> moab::EigenDecomp(moab::Matrix3 >>>> const&, double*, moab::CartVect*)': >>>> >>>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>>> moab::EigenDecomp(moab::Matrix3 >>>> const&, double*, moab::CartVect*)]+0xb7f): >>>> >>>> undefined >>>> reference to `std::cerr' >>>> >>>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>>> moab::EigenDecomp(moab::Matrix3 >>>> const&, double*, moab::CartVect*)]+0xb84): >>>> >>>> undefined >>>> reference to `std::basic_ostream >& >>>> std::operator<< >>>> >(std::basic_ostream >&, char >>>> const*)' >>>> >>>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>>> moab::EigenDecomp(moab::Matrix3 >>>> const&, double*, moab::CartVect*)]+0xb89): >>>> >>>> undefined >>>> reference to `std::basic_ostream >& >>>> std::endl >>>> >(std::basic_ostream >&)' >>>> >>>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>>> moab::EigenDecomp(moab::Matrix3 >>>> const&, double*, moab::CartVect*)]+0xb91): >>>> undefined >>>> reference to `std::basic_ostream >>>>> ::operator<<(std::basic___ostream>>> >>>> std::char_traits >& (*)(std::basic_ostream>>> std::char_traits >&))' >>>> >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o):(.eh_frame+__0x22f): >>>> undefined reference to >>>> >>>> `__gxx_personality_v0' >>>> collect2: ld returned 1 exit status >>>> make: *** [nek5000] Error 1 >>>> >>>> Thanks, >>>> Ami >>>> >>>> >>>> _________________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.__gov >>>> >>>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >>>> >>>> >>>> >>>> -- >>>> ==============================__==============================__==== >>>> >>>> "You will keep in perfect peace him whose mind is >>>> steadfast, because he trusts in you." Isaiah 26:3 >>>> >>>> Tim Tautges Argonne National Laboratory >>>> (tautges at mcs.anl.gov ) >>>> (telecommuting from UW-Madison) >>>> phone (gvoice): (608) 354-1459 1500 >>>> Engineering Dr. >>>> fax: (608) 263-4499 >>>> Madison, WI 53706 >>>> >>>> _________________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.__gov >>>> >>>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>> >>> -- >>> ================================================================ >>> "You will keep in perfect peace him whose mind is >>> steadfast, because he trusts in you." Isaiah 26:3 >>> >>> Tim Tautges Argonne National Laboratory >>> (tautges at mcs.anl.gov) (telecommuting from UW-Madison) >>> phone (gvoice): (608) 354-1459 1500 Engineering Dr. >>> fax: (608) 263-4499 Madison, WI 53706 >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > -- ================================================================ "You will keep in perfect peace him whose mind is steadfast, because he trusts in you." Isaiah 26:3 Tim Tautges Argonne National Laboratory (tautges at mcs.anl.gov) (telecommuting from UW-Madison) phone (gvoice): (608) 354-1459 1500 Engineering Dr. fax: (608) 263-4499 Madison, WI 53706 From nek5000-users at lists.mcs.anl.gov Wed Sep 11 12:10:28 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Sep 2013 12:10:28 -0500 (CDT) Subject: [Nek5000-users] Running MOAB example In-Reply-To: <52309C2A.1000306@mcs.anl.gov> Message-ID: ----- Original Message ----- | Aha, good catch. | Iulian, could you backport the imesh_freememory function? Thanks. Hello, The Version 4.6 was released on February 11. The link to the tar ball is in the web page. http://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB http://ftp.mcs.anl.gov/pub/fathom/moab-4.6.0.tar.gz (so this is the official release 4.6) The current Version4.6 branch, in the git repository, already has the free memory function backported. That tarball is updated nightly, and you can get it from this link (on the moab wiki page too) http://ftp.mcs.anl.gov/pub/fathom/moab-4.6-nightly.tar.gz Is this what they need ? Thanks, Iulian | - tim | On 09/11/2013 11:33 AM, Vijay S. Mahadevan wrote: | > The linker error is because of your version mismatch. You need to | > update your moab to the latest version. I see you are using v4.6 | > now. | > You should be able to use the dev version from | > https://bitbucket.org/fathomteam/moab with git or download the | > newer | > patch from https://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB. | > | > Tim, can we create a new patched version of the release for | > download. | > I spoke to Rajeev about this some time back but we need to decide | > what | > fixes to backport. | > | > Vijay | > | > On Wed, Sep 11, 2013 at 11:20 AM, | > wrote: | >> | >> Yes , I am using gnu, and whwen I add USR_LFLAGS="-lmpi_cxx | >> -lstdc++, | >> I get this, | >> makenek - automatic build tool for Nek5000 | >> generating makefile ... | >> mpif77 -c -O2 -fdefault-real-8 -x f77-cpp-input -fcray-pointer | >> -DMOAB | >> -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG | >> -I/home/amirreza/nek5_svn/amirreza_test/examples/moab | >> -I/home/amirreza/nek5_svn/trunk/nek -I./ | >> /home/amirreza/nek5_svn/amirreza_test/examples/moab/pipe.f | >> -I/home/amirreza/nek5_svn/trunk/nek/3rd_party | >> -I/home/amirreza/Amirreza/moab-4.6.0/gcc/include -o obj/pipe.o | >> mpif77 -o nek5000 obj/pipe.o obj/drive.o obj/drive1.o obj/drive2.o | >> obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o | >> obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o | >> obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o | >> obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o | >> obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o | >> obj/math.o | >> obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o | >> obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o | >> obj/hsmg.o | >> obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o | >> obj/navier6.o | >> obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o | >> obj/byte.o | >> obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o | >> obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o | >> obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o | >> obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o | >> obj/imeshutil.o | >> obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o | >> obj/jl_sort.o | >> obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o | >> obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o | >> obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o | >> obj/jl_obbox.o | >> obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o | >> obj/jl_findpts_el_2.o | >> obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o | >> -L/home/amirreza/Amirreza/netcdf-4.1.3/gcc/lib | >> -L/home/amirreza/Amirreza/zlib-1.2.5/gcc/lib | >> -L/home/amirreza/Amirreza/szip-2.1/gcc/lib | >> -L/home/amirreza/Amirreza/hdf5-1.8.11/lib | >> -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib | >> -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib -liMesh -lMOAB | >> -lnetcdf -lhdf5 | >> -lsz -lm -lmpi_cxx -lstdc++ | >> obj/moab.o: In function `nekmoab_intbc_': | >> moab.f:(.text+0xe9d): undefined reference to `imesh_freememory_' | >> moab.f:(.text+0xece): undefined reference to `imesh_freememory_' | >> moab.f:(.text+0xee4): undefined reference to `imesh_freememory_' | >> moab.f:(.text+0xf05): undefined reference to `imesh_freememory_' | >> obj/moab.o: In function `nekmoab_bc_': | >> moab.f:(.text+0x1306): undefined reference to `imesh_freememory_' | >> | >> collect2: ld returned 1 exit status | >> make: *** [nek5000] Error 1 | >> | >> Thanks, | >> Ami | >> | >> | >> On Wed, Sep 11, 2013 at 12:05 PM, | >> wrote: | >>> | >>> It depends which compiler you're using. Are you using gnu? | >>> | >>> Please send complete compile output. | >>> | >>> - tim | >>> | >>> | >>> On 09/11/2013 10:11 AM, nek5000-users at lists.mcs.anl.gov wrote: | >>>> | >>>> Thanks for your answer, to make sure I have added libraries to | >>>> makenek | >>>> ''USR_LFLAGS="-lmpi_cxx -lstdc++" which I'm | >>>> getting same error,so you mean I need to add appropriate fortran | >>>> library | >>>> to USR_LFLAGS? | >>>> | >>>> Thanks, | >>>> Ami | >>>> | >>>> | >>>> On Wed, Sep 11, 2013 at 10:47 AM, | >>>> >>> > wrote: | >>>> | >>>> Hi Ami, | >>>> That's the C++ runtime. You have two options: | >>>> 1. Link with the C++ compiler; in this case, you'll have to | >>>> explicitly add the fortran runtime libraries to the link | >>>> statement, which is most easily done by adding it to USR_LFLAGS | >>>> in | >>>> makenek. Compiler documents often tell you which | >>>> libraries implement the fortran runtime, usually in a section | >>>> about | >>>> inter-language linking. | >>>> | >>>> 2. Add the C++ std libs to USR_LFLAGS. The trunk/nek/makenek | >>>> file | >>>> has a few examples of this method for | >>>> gnu/intel/pgi. Sometimes, like on BG/x, it can be difficult to | >>>> figure out what all comprises the C++ runtime, which | >>>> is why I list 1. above. | >>>> | >>>> - tim | >>>> | >>>> | >>>> On 09/11/2013 09:31 AM, nek5000-users at lists.mcs.anl.__gov | >>>> wrote: | >>>> | >>>> Hello Neks, | >>>> | >>>> I am trying to run MOAB example with nek5000, but all the time | >>>> which I am running, it gives me set of undefined | >>>> reference error. I put an error with last part of my ./makenek | >>>> pipe log below. | >>>> What is wrong with my work? | >>>> | >>>> IODebugTrack.cpp:(.text+0xb74)__: undefined reference to | >>>> `std::basic_ostream >& | >>>> | >>>> std::operator<< | >>>>> (std::basic_ostream >&, char | >>>>> const*)' | >>>> IODebugTrack.cpp:(.text+0xb7f)__: undefined reference to | >>>> `std::basic_ostream | >>>> >::operator<<(unsigned long)' | >>>> IODebugTrack.cpp:(.text+0xb8c)__: undefined reference to | >>>> `std::basic_ostream >& | >>>> | >>>> std::operator<< | >>>>> (std::basic_ostream >&, char | >>>>> const*)' | >>>> IODebugTrack.cpp:(.text+0xb97)__: undefined reference to | >>>> `std::basic_ostream | >>>> >::operator<<(unsigned long)' | >>>> IODebugTrack.cpp:(.text+0xbd3)__: undefined reference to | >>>> `std::basic_ostream >& | >>>> | >>>> std::operator<< | >>>>> (std::basic_ostream >&, char | >>>>> const*)' | >>>> IODebugTrack.cpp:(.text+0xbde)__: undefined reference to | >>>> `std::basic_ostream | >>>> >::operator<<(unsigned long)' | >>>> IODebugTrack.cpp:(.text+0xbeb)__: undefined reference to | >>>> `std::basic_ostream >& | >>>> | >>>> std::operator<< | >>>>> (std::basic_ostream >&, char | >>>>> const*)' | >>>> IODebugTrack.cpp:(.text+0xbf6)__: undefined reference to | >>>> `std::basic_ostream | >>>> >::operator<<(unsigned long)' | >>>> IODebugTrack.cpp:(.text+0xc03)__: undefined reference to | >>>> `std::basic_ostream >& | >>>> | >>>> std::operator<< | >>>>> (std::basic_ostream >&, char | >>>>> const*)' | >>>> IODebugTrack.cpp:(.text+0xc0e)__: undefined reference to | >>>> `std::basic_ostream | >>>> >::operator<<(unsigned long)' | >>>> IODebugTrack.cpp:(.text+0xc1b)__: undefined reference to | >>>> `std::basic_ostream >& | >>>> | >>>> std::operator<< | >>>>> (std::basic_ostream >&, char | >>>>> const*)' | >>>> IODebugTrack.cpp:(.text+0xc26)__: undefined reference to | >>>> `std::basic_ostream | >>>> >::operator<<(unsigned long)' | >>>> IODebugTrack.cpp:(.text+0xc33)__: undefined reference to | >>>> `std::basic_ostream >& | >>>> | >>>> std::operator<< | >>>>> (std::basic_ostream >&, char | >>>>> const*)' | >>>> IODebugTrack.cpp:(.text+0xc38)__: undefined reference to | >>>> `std::basic_ostream >& | >>>> | >>>> std::endl | >>>> >(std::basic_ostream>>> std::char_traits >&)' | >>>> IODebugTrack.cpp:(.text+0xc40)__: undefined reference to | >>>> `std::basic_ostream | >>>> >::operator<<(std::basic___ostream | >>>>> & (*)(std::basic_ostream>>> std::char_traits >&))' | >>>> IODebugTrack.cpp:(.text+0xc50)__: undefined reference to | >>>> `std::basic_ostream | >>>> >::flush()' | >>>> | >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): | >>>> In | >>>> function | >>>> `moab::IODebugTrack::all___reduce()': | >>>> IODebugTrack.cpp:(.text+0xd08)__: undefined reference to | >>>> `MPI_Comm_size' | >>>> IODebugTrack.cpp:(.text+0xdfe)__: undefined reference to | >>>> `MPI_Gather' | >>>> IODebugTrack.cpp:(.text+__0x1080): undefined reference to | >>>> `MPI_Gatherv' | >>>> | >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): | >>>> In | >>>> function | >>>> `__static_initialization_and___destruction_0(int, int)': | >>>> IODebugTrack.cpp:(.text+__0x1221): undefined reference to | >>>> `std::ios_base::Init::Init()' | >>>> IODebugTrack.cpp:(.text+__0x1226): undefined reference to | >>>> `std::ios_base::Init::~Init()' | >>>> | >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): | >>>> In | >>>> function | >>>> `std::list>>> std::allocator | >>>>> ::_M_insert(std::_List___iterator, | >>>> moab::IODebugTrack::DRange const&)': | >>>> | >>>> IODebugTrack.cpp:(.text.___ZNSt4listIN4moab12IODebugTrack__6DRangeESaIS2_EE9_M___insertESt14_List_iteratorIS2___ERKS2_[std::list>>> std::allocator | >>>>> ::_M_insert(std::_List___iterator, | >>>> | >>>> moab::IODebugTrack::DRange const&)]+0x3a): undefined reference | >>>> to | >>>> | >>>> `std::__detail::_List_node___base::_M_hook(std::__detail::___List_node_base*)' | >>>> | >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): | >>>> In | >>>> function | >>>> | >>>> `__gnu_cxx::new_allocator | >>>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, | >>>> unsigned long)': | >>>> | >>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE10deallocateEPS5_m[__gnu___cxx::new_allocator | >>>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, | >>>> unsigned long)]+0x1c): undefined reference to | >>>> `operator | >>>> delete(void*)' | >>>> | >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): | >>>> In | >>>> function | >>>> | >>>> `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__allocate(unsigned | >>>> long, void const*)': | >>>> | >>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned | >>>> | >>>> long, void const*)]+0x2c): undefined reference to | >>>> `std::__throw_bad_alloc()' | >>>> | >>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned | >>>> | >>>> long, void const*)]+0x45): undefined reference to `operator | >>>> new(unsigned long)' | >>>> | >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): | >>>> In | >>>> function | >>>> | >>>> `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__deallocate(moab::IODebugTrack:__:DRange*, | >>>> unsigned | >>>> long)': | >>>> | >>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE10deallocateEPS3_m[____gnu_cxx::new_allocator::__deallocate(moab::IODebugTrack:__:DRange*, | >>>> | >>>> unsigned long)]+0x1c): undefined reference to `operator | >>>> delete(void*)' | >>>> | >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): | >>>> In | >>>> function | >>>> | >>>> `__gnu_cxx::new_allocator | >>>>> ::allocate(unsigned long, void const*)': | >>>> | >>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator | >>>> | >>>> >::allocate(unsigned long, void const*)]+0x2c): undefined | >>>> reference to `std::__throw_bad_alloc()' | >>>> | >>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator | >>>> | >>>> >::allocate(unsigned long, void const*)]+0x46): undefined | >>>> reference to `operator new(unsigned long)' | >>>> | >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o):(.eh_frame+__0x24b): | >>>> undefined reference to | >>>> `__gxx_personality_v0' | >>>> | >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): | >>>> In | >>>> function | >>>> `moab::operator<<(std::basic___ostream>>> std::char_traits >&, moab::OrientedBox const&)': | >>>> | >>>> OrientedBox.cpp:(.text+0x97): undefined reference to | >>>> `std::basic_ostream >& | >>>> std::operator<< | >>>> >(std::basic_ostream>>> std::char_traits >&, char const*)' | >>>> OrientedBox.cpp:(.text+0xaf): undefined reference to | >>>> `std::basic_ostream >& | >>>> std::operator<< | >>>> >(std::basic_ostream>>> std::char_traits >&, char const*)' | >>>> OrientedBox.cpp:(.text+0xbc): undefined reference to | >>>> `std::basic_ostream | >>>> >::operator<<(double)' | >>>> OrientedBox.cpp:(.text+0xc9): undefined reference to | >>>> `std::basic_ostream >& | >>>> std::operator<< | >>>> >(std::basic_ostream>>> std::char_traits >&, char const*)' | >>>> OrientedBox.cpp:(.text+0xe1): undefined reference to | >>>> `std::basic_ostream >& | >>>> std::operator<< | >>>> >(std::basic_ostream>>> std::char_traits >&, char const*)' | >>>> OrientedBox.cpp:(.text+0xee): undefined reference to | >>>> `std::basic_ostream | >>>> >::operator<<(double)' | >>>> OrientedBox.cpp:(.text+0xfb): undefined reference to | >>>> `std::basic_ostream >& | >>>> std::operator<< | >>>> >(std::basic_ostream>>> std::char_traits >&, char const*)' | >>>> OrientedBox.cpp:(.text+0x113): undefined reference to | >>>> `std::basic_ostream >& | >>>> std::operator<< | >>>>> (std::basic_ostream >&, char | >>>>> const*)' | >>>> OrientedBox.cpp:(.text+0x120): undefined reference to | >>>> `std::basic_ostream | >>>> >::operator<<(double)' | >>>> | >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): | >>>> In | >>>> function | >>>> `__static_initialization_and___destruction_0(int, int)': | >>>> OrientedBox.cpp:(.text+0x3aaf)__: undefined reference to | >>>> `std::ios_base::Init::Init()' | >>>> OrientedBox.cpp:(.text+0x3ab4)__: undefined reference to | >>>> `std::ios_base::Init::~Init()' | >>>> | >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): | >>>> In | >>>> function `moab::ErrorCode | >>>> moab::EigenDecomp(moab::Matrix3 | >>>> const&, double*, moab::CartVect*)': | >>>> | >>>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode | >>>> moab::EigenDecomp(moab::Matrix3 | >>>> const&, double*, moab::CartVect*)]+0xb7f): | >>>> | >>>> undefined | >>>> reference to `std::cerr' | >>>> | >>>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode | >>>> moab::EigenDecomp(moab::Matrix3 | >>>> const&, double*, moab::CartVect*)]+0xb84): | >>>> | >>>> undefined | >>>> reference to `std::basic_ostream >& | >>>> std::operator<< | >>>> >(std::basic_ostream >&, char | >>>> const*)' | >>>> | >>>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode | >>>> moab::EigenDecomp(moab::Matrix3 | >>>> const&, double*, moab::CartVect*)]+0xb89): | >>>> | >>>> undefined | >>>> reference to `std::basic_ostream >& | >>>> std::endl | >>>> >(std::basic_ostream >&)' | >>>> | >>>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode | >>>> moab::EigenDecomp(moab::Matrix3 | >>>> const&, double*, moab::CartVect*)]+0xb91): | >>>> undefined | >>>> reference to `std::basic_ostream | >>>>> ::operator<<(std::basic___ostream>>> | >>>> std::char_traits >& (*)(std::basic_ostream>>> std::char_traits >&))' | >>>> | >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o):(.eh_frame+__0x22f): | >>>> undefined reference to | >>>> | >>>> `__gxx_personality_v0' | >>>> collect2: ld returned 1 exit status | >>>> make: *** [nek5000] Error 1 | >>>> | >>>> Thanks, | >>>> Ami | >>>> | >>>> | >>>> _________________________________________________ | >>>> Nek5000-users mailing list | >>>> Nek5000-users at lists.mcs.anl.__gov | >>>> | >>>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users | >>>> | >>>> | >>>> | >>>> -- | >>>> ==============================__==============================__==== | >>>> | >>>> "You will keep in perfect peace him whose mind is | >>>> steadfast, because he trusts in you." Isaiah 26:3 | >>>> | >>>> Tim Tautges Argonne National Laboratory | >>>> (tautges at mcs.anl.gov ) | >>>> (telecommuting from UW-Madison) | >>>> phone (gvoice): (608) 354-1459 1500 | >>>> Engineering Dr. | >>>> fax: (608) 263-4499 | >>>> Madison, WI 53706 | >>>> | >>>> _________________________________________________ | >>>> Nek5000-users mailing list | >>>> Nek5000-users at lists.mcs.anl.__gov | >>>> | >>>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users | >>>> | >>>> | >>>> | >>>> | >>>> | >>>> | >>>> _______________________________________________ | >>>> Nek5000-users mailing list | >>>> Nek5000-users at lists.mcs.anl.gov | >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | >>>> | >>> | >>> -- | >>> ================================================================ | >>> "You will keep in perfect peace him whose mind is | >>> steadfast, because he trusts in you." Isaiah 26:3 | >>> | >>> Tim Tautges Argonne National Laboratory | >>> (tautges at mcs.anl.gov) (telecommuting from UW-Madison) | >>> phone (gvoice): (608) 354-1459 1500 Engineering Dr. | >>> fax: (608) 263-4499 Madison, WI 53706 | >>> | >>> _______________________________________________ | >>> Nek5000-users mailing list | >>> Nek5000-users at lists.mcs.anl.gov | >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | >> | >> | >> | >> _______________________________________________ | >> Nek5000-users mailing list | >> Nek5000-users at lists.mcs.anl.gov | >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | >> | > | -- | ================================================================ | "You will keep in perfect peace him whose mind is | steadfast, because he trusts in you." Isaiah 26:3 | Tim Tautges Argonne National Laboratory | (tautges at mcs.anl.gov) (telecommuting from UW-Madison) | phone (gvoice): (608) 354-1459 1500 Engineering Dr. | fax: (608) 263-4499 Madison, WI 53706 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Sep 11 12:17:40 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Sep 2013 12:17:40 -0500 Subject: [Nek5000-users] Running MOAB example In-Reply-To: <192817286.8839645.1378919428460.JavaMail.root@mcs.anl.gov> References: <52309C2A.1000306@mcs.anl.gov> <192817286.8839645.1378919428460.JavaMail.root@mcs.anl.gov> Message-ID: > http://ftp.mcs.anl.gov/pub/fathom/moab-4.6-nightly.tar.gz > > Is this what they need? Yes. But can you also replace the link to moab-4.6.0.tar.gz with the nightly and rename with a patch number like: 4.6.1. That should give better tractability for future version related queries. Vijay On Wed, Sep 11, 2013 at 12:10 PM, Iulian Grindeanu wrote: > > > ________________________________ > > Aha, good catch. > > Iulian, could you backport the imesh_freememory function? Thanks. > > Hello, > The Version 4.6 was released on February 11. The link to the tar ball is in > the web page. > http://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB > > http://ftp.mcs.anl.gov/pub/fathom/moab-4.6.0.tar.gz > (so this is the official release 4.6) > > The current Version4.6 branch, in the git repository, already has the free > memory function backported. > That tarball is updated nightly, and you can get it from this link (on the > moab wiki page too) > > http://ftp.mcs.anl.gov/pub/fathom/moab-4.6-nightly.tar.gz > > Is this what they need? > > Thanks, > Iulian > > > > - tim > > On 09/11/2013 11:33 AM, Vijay S. Mahadevan wrote: >> The linker error is because of your version mismatch. You need to >> update your moab to the latest version. I see you are using v4.6 now. >> You should be able to use the dev version from >> https://bitbucket.org/fathomteam/moab with git or download the newer >> patch from https://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB. >> >> Tim, can we create a new patched version of the release for download. >> I spoke to Rajeev about this some time back but we need to decide what >> fixes to backport. >> >> Vijay >> >> On Wed, Sep 11, 2013 at 11:20 AM, >> wrote: >>> >>> Yes , I am using gnu, and whwen I add USR_LFLAGS="-lmpi_cxx -lstdc++, >>> I get this, >>> makenek - automatic build tool for Nek5000 >>> generating makefile ... >>> mpif77 -c -O2 -fdefault-real-8 -x f77-cpp-input -fcray-pointer -DMOAB >>> -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG >>> -I/home/amirreza/nek5_svn/amirreza_test/examples/moab >>> -I/home/amirreza/nek5_svn/trunk/nek -I./ >>> /home/amirreza/nek5_svn/amirreza_test/examples/moab/pipe.f >>> -I/home/amirreza/nek5_svn/trunk/nek/3rd_party >>> -I/home/amirreza/Amirreza/moab-4.6.0/gcc/include -o obj/pipe.o >>> mpif77 -o nek5000 obj/pipe.o obj/drive.o obj/drive1.o obj/drive2.o >>> obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o >>> obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o >>> obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o >>> obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o >>> obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o >>> obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o >>> obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o >>> obj/hsmg.o >>> obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o >>> obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o >>> obj/byte.o >>> obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o >>> obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o >>> obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o >>> obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o obj/imeshutil.o >>> obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o >>> obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o >>> obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o >>> obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o >>> obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o >>> obj/jl_findpts_el_2.o >>> obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o >>> -L/home/amirreza/Amirreza/netcdf-4.1.3/gcc/lib >>> -L/home/amirreza/Amirreza/zlib-1.2.5/gcc/lib >>> -L/home/amirreza/Amirreza/szip-2.1/gcc/lib >>> -L/home/amirreza/Amirreza/hdf5-1.8.11/lib >>> -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib >>> -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib -liMesh -lMOAB -lnetcdf >>> -lhdf5 >>> -lsz -lm -lmpi_cxx -lstdc++ >>> obj/moab.o: In function `nekmoab_intbc_': >>> moab.f:(.text+0xe9d): undefined reference to `imesh_freememory_' >>> moab.f:(.text+0xece): undefined reference to `imesh_freememory_' >>> moab.f:(.text+0xee4): undefined reference to `imesh_freememory_' >>> moab.f:(.text+0xf05): undefined reference to `imesh_freememory_' >>> obj/moab.o: In function `nekmoab_bc_': >>> moab.f:(.text+0x1306): undefined reference to `imesh_freememory_' >>> >>> collect2: ld returned 1 exit status >>> make: *** [nek5000] Error 1 >>> >>> Thanks, >>> Ami >>> >>> >>> On Wed, Sep 11, 2013 at 12:05 PM, >>> wrote: >>>> >>>> It depends which compiler you're using. Are you using gnu? >>>> >>>> Please send complete compile output. >>>> >>>> - tim >>>> >>>> >>>> On 09/11/2013 10:11 AM, nek5000-users at lists.mcs.anl.gov wrote: >>>>> >>>>> Thanks for your answer, to make sure I have added libraries to makenek >>>>> ''USR_LFLAGS="-lmpi_cxx -lstdc++" which I'm >>>>> getting same error,so you mean I need to add appropriate fortran >>>>> library >>>>> to USR_LFLAGS? >>>>> >>>>> Thanks, >>>>> Ami >>>>> >>>>> >>>>> On Wed, Sep 11, 2013 at 10:47 AM, >>>> > wrote: >>>>> >>>>> Hi Ami, >>>>> That's the C++ runtime. You have two options: >>>>> 1. Link with the C++ compiler; in this case, you'll have to >>>>> explicitly add the fortran runtime libraries to the link >>>>> statement, which is most easily done by adding it to USR_LFLAGS in >>>>> makenek. Compiler documents often tell you which >>>>> libraries implement the fortran runtime, usually in a section >>>>> about >>>>> inter-language linking. >>>>> >>>>> 2. Add the C++ std libs to USR_LFLAGS. The trunk/nek/makenek file >>>>> has a few examples of this method for >>>>> gnu/intel/pgi. Sometimes, like on BG/x, it can be difficult to >>>>> figure out what all comprises the C++ runtime, which >>>>> is why I list 1. above. >>>>> >>>>> - tim >>>>> >>>>> >>>>> On 09/11/2013 09:31 AM, nek5000-users at lists.mcs.anl.__gov >>>>> wrote: >>>>> >>>>> Hello Neks, >>>>> >>>>> I am trying to run MOAB example with nek5000, but all the time >>>>> which I am running, it gives me set of undefined >>>>> reference error. I put an error with last part of my ./makenek >>>>> pipe log below. >>>>> What is wrong with my work? >>>>> >>>>> IODebugTrack.cpp:(.text+0xb74)__: undefined reference to >>>>> `std::basic_ostream >& >>>>> >>>>> std::operator<< >>>>>> (std::basic_ostream >&, char const*)' >>>>> IODebugTrack.cpp:(.text+0xb7f)__: undefined reference to >>>>> `std::basic_ostream >>>>> >::operator<<(unsigned long)' >>>>> IODebugTrack.cpp:(.text+0xb8c)__: undefined reference to >>>>> `std::basic_ostream >& >>>>> >>>>> std::operator<< >>>>>> (std::basic_ostream >&, char const*)' >>>>> IODebugTrack.cpp:(.text+0xb97)__: undefined reference to >>>>> `std::basic_ostream >>>>> >::operator<<(unsigned long)' >>>>> IODebugTrack.cpp:(.text+0xbd3)__: undefined reference to >>>>> `std::basic_ostream >& >>>>> >>>>> std::operator<< >>>>>> (std::basic_ostream >&, char const*)' >>>>> IODebugTrack.cpp:(.text+0xbde)__: undefined reference to >>>>> `std::basic_ostream >>>>> >::operator<<(unsigned long)' >>>>> IODebugTrack.cpp:(.text+0xbeb)__: undefined reference to >>>>> `std::basic_ostream >& >>>>> >>>>> std::operator<< >>>>>> (std::basic_ostream >&, char const*)' >>>>> IODebugTrack.cpp:(.text+0xbf6)__: undefined reference to >>>>> `std::basic_ostream >>>>> >::operator<<(unsigned long)' >>>>> IODebugTrack.cpp:(.text+0xc03)__: undefined reference to >>>>> `std::basic_ostream >& >>>>> >>>>> std::operator<< >>>>>> (std::basic_ostream >&, char const*)' >>>>> IODebugTrack.cpp:(.text+0xc0e)__: undefined reference to >>>>> `std::basic_ostream >>>>> >::operator<<(unsigned long)' >>>>> IODebugTrack.cpp:(.text+0xc1b)__: undefined reference to >>>>> `std::basic_ostream >& >>>>> >>>>> std::operator<< >>>>>> (std::basic_ostream >&, char const*)' >>>>> IODebugTrack.cpp:(.text+0xc26)__: undefined reference to >>>>> `std::basic_ostream >>>>> >::operator<<(unsigned long)' >>>>> IODebugTrack.cpp:(.text+0xc33)__: undefined reference to >>>>> `std::basic_ostream >& >>>>> >>>>> std::operator<< >>>>>> (std::basic_ostream >&, char const*)' >>>>> IODebugTrack.cpp:(.text+0xc38)__: undefined reference to >>>>> `std::basic_ostream >& >>>>> >>>>> std::endl >>>>> >(std::basic_ostream>>>> std::char_traits >&)' >>>>> IODebugTrack.cpp:(.text+0xc40)__: undefined reference to >>>>> `std::basic_ostream >>>>> >::operator<<(std::basic___ostream>>>> std::char_traits >>>>>> & (*)(std::basic_ostream>>>> std::char_traits >&))' >>>>> IODebugTrack.cpp:(.text+0xc50)__: undefined reference to >>>>> `std::basic_ostream >>>>> >::flush()' >>>>> >>>>> >>>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>>>> function >>>>> `moab::IODebugTrack::all___reduce()': >>>>> IODebugTrack.cpp:(.text+0xd08)__: undefined reference to >>>>> `MPI_Comm_size' >>>>> IODebugTrack.cpp:(.text+0xdfe)__: undefined reference to >>>>> `MPI_Gather' >>>>> IODebugTrack.cpp:(.text+__0x1080): undefined reference to >>>>> `MPI_Gatherv' >>>>> >>>>> >>>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>>>> function >>>>> `__static_initialization_and___destruction_0(int, int)': >>>>> IODebugTrack.cpp:(.text+__0x1221): undefined reference to >>>>> `std::ios_base::Init::Init()' >>>>> IODebugTrack.cpp:(.text+__0x1226): undefined reference to >>>>> `std::ios_base::Init::~Init()' >>>>> >>>>> >>>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>>>> function >>>>> `std::list>>>> std::allocator >>>>>> ::_M_insert(std::_List___iterator, >>>>> moab::IODebugTrack::DRange const&)': >>>>> >>>>> >>>>> IODebugTrack.cpp:(.text.___ZNSt4listIN4moab12IODebugTrack__6DRangeESaIS2_EE9_M___insertESt14_List_iteratorIS2___ERKS2_[std::list>>>> std::allocator >>>>>> ::_M_insert(std::_List___iterator, >>>>> >>>>> moab::IODebugTrack::DRange const&)]+0x3a): undefined reference >>>>> to >>>>> >>>>> >>>>> `std::__detail::_List_node___base::_M_hook(std::__detail::___List_node_base*)' >>>>> >>>>> >>>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>>>> function >>>>> >>>>> >>>>> `__gnu_cxx::new_allocator >>>>> >>>>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, >>>>> unsigned long)': >>>>> >>>>> >>>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE10deallocateEPS5_m[__gnu___cxx::new_allocator >>>>> >>>>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, >>>>> unsigned long)]+0x1c): undefined reference to >>>>> `operator >>>>> delete(void*)' >>>>> >>>>> >>>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>>>> function >>>>> >>>>> >>>>> `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__allocate(unsigned >>>>> long, void const*)': >>>>> >>>>> >>>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned >>>>> >>>>> long, void const*)]+0x2c): undefined reference to >>>>> `std::__throw_bad_alloc()' >>>>> >>>>> >>>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned >>>>> >>>>> long, void const*)]+0x45): undefined reference to `operator >>>>> new(unsigned long)' >>>>> >>>>> >>>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>>>> function >>>>> >>>>> >>>>> `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__deallocate(moab::IODebugTrack:__:DRange*, >>>>> unsigned >>>>> long)': >>>>> >>>>> >>>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE10deallocateEPS3_m[____gnu_cxx::new_allocator::__deallocate(moab::IODebugTrack:__:DRange*, >>>>> >>>>> unsigned long)]+0x1c): undefined reference to `operator >>>>> delete(void*)' >>>>> >>>>> >>>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>>>> function >>>>> >>>>> >>>>> `__gnu_cxx::new_allocator >>>>>> ::allocate(unsigned long, void const*)': >>>>> >>>>> >>>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator >>>>> >>>>> >::allocate(unsigned long, void const*)]+0x2c): undefined >>>>> reference to `std::__throw_bad_alloc()' >>>>> >>>>> >>>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator >>>>> >>>>> >::allocate(unsigned long, void const*)]+0x46): undefined >>>>> reference to `operator new(unsigned long)' >>>>> >>>>> >>>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o):(.eh_frame+__0x24b): >>>>> undefined reference to >>>>> `__gxx_personality_v0' >>>>> >>>>> >>>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In >>>>> function >>>>> `moab::operator<<(std::basic___ostream>>>> std::char_traits >&, moab::OrientedBox const&)': >>>>> >>>>> OrientedBox.cpp:(.text+0x97): undefined reference to >>>>> `std::basic_ostream >& >>>>> std::operator<< >>>>> >(std::basic_ostream>>>> std::char_traits >&, char const*)' >>>>> OrientedBox.cpp:(.text+0xaf): undefined reference to >>>>> `std::basic_ostream >& >>>>> std::operator<< >>>>> >(std::basic_ostream>>>> std::char_traits >&, char const*)' >>>>> OrientedBox.cpp:(.text+0xbc): undefined reference to >>>>> `std::basic_ostream >>>>> >::operator<<(double)' >>>>> OrientedBox.cpp:(.text+0xc9): undefined reference to >>>>> `std::basic_ostream >& >>>>> std::operator<< >>>>> >(std::basic_ostream>>>> std::char_traits >&, char const*)' >>>>> OrientedBox.cpp:(.text+0xe1): undefined reference to >>>>> `std::basic_ostream >& >>>>> std::operator<< >>>>> >(std::basic_ostream>>>> std::char_traits >&, char const*)' >>>>> OrientedBox.cpp:(.text+0xee): undefined reference to >>>>> `std::basic_ostream >>>>> >::operator<<(double)' >>>>> OrientedBox.cpp:(.text+0xfb): undefined reference to >>>>> `std::basic_ostream >& >>>>> std::operator<< >>>>> >(std::basic_ostream>>>> std::char_traits >&, char const*)' >>>>> OrientedBox.cpp:(.text+0x113): undefined reference to >>>>> `std::basic_ostream >& >>>>> std::operator<< >>>>>> (std::basic_ostream >&, char const*)' >>>>> OrientedBox.cpp:(.text+0x120): undefined reference to >>>>> `std::basic_ostream >>>>> >::operator<<(double)' >>>>> >>>>> >>>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In >>>>> function >>>>> `__static_initialization_and___destruction_0(int, int)': >>>>> OrientedBox.cpp:(.text+0x3aaf)__: undefined reference to >>>>> `std::ios_base::Init::Init()' >>>>> OrientedBox.cpp:(.text+0x3ab4)__: undefined reference to >>>>> `std::ios_base::Init::~Init()' >>>>> >>>>> >>>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In >>>>> function `moab::ErrorCode >>>>> moab::EigenDecomp>>>> moab::CartVect>(moab::Matrix3 >>>>> const&, double*, moab::CartVect*)': >>>>> >>>>> >>>>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>>>> moab::EigenDecomp>>>> moab::CartVect>(moab::Matrix3 >>>>> const&, double*, moab::CartVect*)]+0xb7f): >>>>> >>>>> undefined >>>>> reference to `std::cerr' >>>>> >>>>> >>>>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>>>> moab::EigenDecomp>>>> moab::CartVect>(moab::Matrix3 >>>>> const&, double*, moab::CartVect*)]+0xb84): >>>>> >>>>> undefined >>>>> reference to `std::basic_ostream >>>>> >& >>>>> std::operator<< >>>>> >(std::basic_ostream >&, char >>>>> const*)' >>>>> >>>>> >>>>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>>>> moab::EigenDecomp>>>> moab::CartVect>(moab::Matrix3 >>>>> const&, double*, moab::CartVect*)]+0xb89): >>>>> >>>>> undefined >>>>> reference to `std::basic_ostream >>>>> >& >>>>> std::endl >>>>> >(std::basic_ostream >&)' >>>>> >>>>> >>>>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>>>> moab::EigenDecomp>>>> moab::CartVect>(moab::Matrix3 >>>>> const&, double*, moab::CartVect*)]+0xb91): >>>>> undefined >>>>> reference to `std::basic_ostream >>>>>> ::operator<<(std::basic___ostream>>>> >>>>> std::char_traits >& (*)(std::basic_ostream>>>> std::char_traits >&))' >>>>> >>>>> >>>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o):(.eh_frame+__0x22f): >>>>> undefined reference to >>>>> >>>>> `__gxx_personality_v0' >>>>> collect2: ld returned 1 exit status >>>>> make: *** [nek5000] Error 1 >>>>> >>>>> Thanks, >>>>> Ami >>>>> >>>>> >>>>> _________________________________________________ >>>>> Nek5000-users mailing list >>>>> Nek5000-users at lists.mcs.anl.__gov >>>>> >>>>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> ==============================__==============================__==== >>>>> >>>>> "You will keep in perfect peace him whose mind is >>>>> steadfast, because he trusts in you." Isaiah 26:3 >>>>> >>>>> Tim Tautges Argonne National Laboratory >>>>> (tautges at mcs.anl.gov ) >>>>> (telecommuting from UW-Madison) >>>>> phone (gvoice): (608) 354-1459 >>>>> 1500 >>>>> Engineering Dr. >>>>> fax: (608) 263-4499 >>>>> Madison, WI 53706 >>>>> >>>>> _________________________________________________ >>>>> Nek5000-users mailing list >>>>> Nek5000-users at lists.mcs.anl.__gov >>>>> >>>>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Nek5000-users mailing list >>>>> Nek5000-users at lists.mcs.anl.gov >>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>> >>>> >>>> -- >>>> ================================================================ >>>> "You will keep in perfect peace him whose mind is >>>> steadfast, because he trusts in you." Isaiah 26:3 >>>> >>>> Tim Tautges Argonne National Laboratory >>>> (tautges at mcs.anl.gov) (telecommuting from UW-Madison) >>>> phone (gvoice): (608) 354-1459 1500 Engineering Dr. >>>> fax: (608) 263-4499 Madison, WI 53706 >>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> > > -- > ================================================================ > "You will keep in perfect peace him whose mind is > steadfast, because he trusts in you." Isaiah 26:3 > > Tim Tautges Argonne National Laboratory > (tautges at mcs.anl.gov) (telecommuting from UW-Madison) > phone (gvoice): (608) 354-1459 1500 Engineering Dr. > fax: (608) 263-4499 Madison, WI 53706 > > From nek5000-users at lists.mcs.anl.gov Wed Sep 11 12:30:38 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Sep 2013 12:30:38 -0500 Subject: [Nek5000-users] Running MOAB example In-Reply-To: <192817286.8839645.1378919428460.JavaMail.root@mcs.anl.gov> References: <192817286.8839645.1378919428460.JavaMail.root@mcs.anl.gov> Message-ID: On 09/11/2013 12:10 PM, Iulian Grindeanu wrote: > > > ------------------------------------------------------------------------------------------------------------------------ > > Aha, good catch. > > Iulian, could you backport the imesh_freememory function? Thanks. > > Hello, > The Version 4.6 was released on February 11. The link to the tar ball is in the web page. > http://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB > > http://ftp.mcs.anl.gov/pub/fathom/moab-4.6.0.tar.gz > (so this is the official release 4.6) > > The current Version4.6 branch, in the git repository, already has the free memory function backported. > That tarball is updated nightly, and you can get it from this link (on the moab wiki page too) > > http://ftp.mcs.anl.gov/pub/fathom/moab-4.6-nightly.tar.gz > > Is this what they need? > Ok, yes, that's what they need, thanks. - tim > Thanks, > Iulian > > - tim > > On 09/11/2013 11:33 AM, Vijay S. Mahadevan wrote: > > The linker error is because of your version mismatch. You need to > > update your moab to the latest version. I see you are using v4.6 now. > > You should be able to use the dev version from > > https://bitbucket.org/fathomteam/moab with git or download the newer > > patch from https://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB. > > > > Tim, can we create a new patched version of the release for download. > > I spoke to Rajeev about this some time back but we need to decide what > > fixes to backport. > > > > Vijay > > > > On Wed, Sep 11, 2013 at 11:20 AM, wrote: > >> > >> Yes , I am using gnu, and whwen I add USR_LFLAGS="-lmpi_cxx -lstdc++, > >> I get this, > >> makenek - automatic build tool for Nek5000 > >> generating makefile ... > >> mpif77 -c -O2 -fdefault-real-8 -x f77-cpp-input -fcray-pointer -DMOAB > >> -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG > >> -I/home/amirreza/nek5_svn/amirreza_test/examples/moab > >> -I/home/amirreza/nek5_svn/trunk/nek -I./ > >> /home/amirreza/nek5_svn/amirreza_test/examples/moab/pipe.f > >> -I/home/amirreza/nek5_svn/trunk/nek/3rd_party > >> -I/home/amirreza/Amirreza/moab-4.6.0/gcc/include -o obj/pipe.o > >> mpif77 -o nek5000 obj/pipe.o obj/drive.o obj/drive1.o obj/drive2.o > >> obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o > >> obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o > >> obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o > >> obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o > >> obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o > >> obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o > >> obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o obj/hsmg.o > >> obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o > >> obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o obj/byte.o > >> obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o > >> obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o > >> obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o > >> obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o obj/imeshutil.o > >> obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o > >> obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o > >> obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o > >> obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o > >> obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o obj/jl_findpts_el_2.o > >> obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o > >> -L/home/amirreza/Amirreza/netcdf-4.1.3/gcc/lib > >> -L/home/amirreza/Amirreza/zlib-1.2.5/gcc/lib > >> -L/home/amirreza/Amirreza/szip-2.1/gcc/lib > >> -L/home/amirreza/Amirreza/hdf5-1.8.11/lib > >> -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib > >> -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib -liMesh -lMOAB -lnetcdf -lhdf5 > >> -lsz -lm -lmpi_cxx -lstdc++ > >> obj/moab.o: In function `nekmoab_intbc_': > >> moab.f:(.text+0xe9d): undefined reference to `imesh_freememory_' > >> moab.f:(.text+0xece): undefined reference to `imesh_freememory_' > >> moab.f:(.text+0xee4): undefined reference to `imesh_freememory_' > >> moab.f:(.text+0xf05): undefined reference to `imesh_freememory_' > >> obj/moab.o: In function `nekmoab_bc_': > >> moab.f:(.text+0x1306): undefined reference to `imesh_freememory_' > >> > >> collect2: ld returned 1 exit status > >> make: *** [nek5000] Error 1 > >> > >> Thanks, > >> Ami > >> > >> > >> On Wed, Sep 11, 2013 at 12:05 PM, wrote: > >>> > >>> It depends which compiler you're using. Are you using gnu? > >>> > >>> Please send complete compile output. > >>> > >>> - tim > >>> > >>> > >>> On 09/11/2013 10:11 AM, nek5000-users at lists.mcs.anl.gov wrote: > >>>> > >>>> Thanks for your answer, to make sure I have added libraries to makenek > >>>> ''USR_LFLAGS="-lmpi_cxx -lstdc++" which I'm > >>>> getting same error,so you mean I need to add appropriate fortran library > >>>> to USR_LFLAGS? > >>>> > >>>> Thanks, > >>>> Ami > >>>> > >>>> > >>>> On Wed, Sep 11, 2013 at 10:47 AM, >>>> > wrote: > >>>> > >>>> Hi Ami, > >>>> That's the C++ runtime. You have two options: > >>>> 1. Link with the C++ compiler; in this case, you'll have to > >>>> explicitly add the fortran runtime libraries to the link > >>>> statement, which is most easily done by adding it to USR_LFLAGS in > >>>> makenek. Compiler documents often tell you which > >>>> libraries implement the fortran runtime, usually in a section about > >>>> inter-language linking. > >>>> > >>>> 2. Add the C++ std libs to USR_LFLAGS. The trunk/nek/makenek file > >>>> has a few examples of this method for > >>>> gnu/intel/pgi. Sometimes, like on BG/x, it can be difficult to > >>>> figure out what all comprises the C++ runtime, which > >>>> is why I list 1. above. > >>>> > >>>> - tim > >>>> > >>>> > >>>> On 09/11/2013 09:31 AM, nek5000-users at lists.mcs.anl.__gov > >>>> wrote: > >>>> > >>>> Hello Neks, > >>>> > >>>> I am trying to run MOAB example with nek5000, but all the time > >>>> which I am running, it gives me set of undefined > >>>> reference error. I put an error with last part of my ./makenek > >>>> pipe log below. > >>>> What is wrong with my work? > >>>> > >>>> IODebugTrack.cpp:(.text+0xb74)__: undefined reference to > >>>> `std::basic_ostream >& > >>>> > >>>> std::operator<< > >>>>> (std::basic_ostream >&, char const*)' > >>>> IODebugTrack.cpp:(.text+0xb7f)__: undefined reference to > >>>> `std::basic_ostream > >>>> >::operator<<(unsigned long)' > >>>> IODebugTrack.cpp:(.text+0xb8c)__: undefined reference to > >>>> `std::basic_ostream >& > >>>> > >>>> std::operator<< > >>>>> (std::basic_ostream >&, char const*)' > >>>> IODebugTrack.cpp:(.text+0xb97)__: undefined reference to > >>>> `std::basic_ostream > >>>> >::operator<<(unsigned long)' > >>>> IODebugTrack.cpp:(.text+0xbd3)__: undefined reference to > >>>> `std::basic_ostream >& > >>>> > >>>> std::operator<< > >>>>> (std::basic_ostream >&, char const*)' > >>>> IODebugTrack.cpp:(.text+0xbde)__: undefined reference to > >>>> `std::basic_ostream > >>>> >::operator<<(unsigned long)' > >>>> IODebugTrack.cpp:(.text+0xbeb)__: undefined reference to > >>>> `std::basic_ostream >& > >>>> > >>>> std::operator<< > >>>>> (std::basic_ostream >&, char const*)' > >>>> IODebugTrack.cpp:(.text+0xbf6)__: undefined reference to > >>>> `std::basic_ostream > >>>> >::operator<<(unsigned long)' > >>>> IODebugTrack.cpp:(.text+0xc03)__: undefined reference to > >>>> `std::basic_ostream >& > >>>> > >>>> std::operator<< > >>>>> (std::basic_ostream >&, char const*)' > >>>> IODebugTrack.cpp:(.text+0xc0e)__: undefined reference to > >>>> `std::basic_ostream > >>>> >::operator<<(unsigned long)' > >>>> IODebugTrack.cpp:(.text+0xc1b)__: undefined reference to > >>>> `std::basic_ostream >& > >>>> > >>>> std::operator<< > >>>>> (std::basic_ostream >&, char const*)' > >>>> IODebugTrack.cpp:(.text+0xc26)__: undefined reference to > >>>> `std::basic_ostream > >>>> >::operator<<(unsigned long)' > >>>> IODebugTrack.cpp:(.text+0xc33)__: undefined reference to > >>>> `std::basic_ostream >& > >>>> > >>>> std::operator<< > >>>>> (std::basic_ostream >&, char const*)' > >>>> IODebugTrack.cpp:(.text+0xc38)__: undefined reference to > >>>> `std::basic_ostream >& > >>>> > >>>> std::endl >(std::basic_ostream >>>> std::char_traits >&)' > >>>> IODebugTrack.cpp:(.text+0xc40)__: undefined reference to > >>>> `std::basic_ostream > >>>> >::operator<<(std::basic___ostream > >>>>> & (*)(std::basic_ostream >>>> std::char_traits >&))' > >>>> IODebugTrack.cpp:(.text+0xc50)__: undefined reference to > >>>> `std::basic_ostream > >>>> >::flush()' > >>>> > >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In > >>>> function > >>>> `moab::IODebugTrack::all___reduce()': > >>>> IODebugTrack.cpp:(.text+0xd08)__: undefined reference to > >>>> `MPI_Comm_size' > >>>> IODebugTrack.cpp:(.text+0xdfe)__: undefined reference to > >>>> `MPI_Gather' > >>>> IODebugTrack.cpp:(.text+__0x1080): undefined reference to > >>>> `MPI_Gatherv' > >>>> > >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In > >>>> function > >>>> `__static_initialization_and___destruction_0(int, int)': > >>>> IODebugTrack.cpp:(.text+__0x1221): undefined reference to > >>>> `std::ios_base::Init::Init()' > >>>> IODebugTrack.cpp:(.text+__0x1226): undefined reference to > >>>> `std::ios_base::Init::~Init()' > >>>> > >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In > >>>> function > >>>> `std::list >>>> std::allocator > >>>>> ::_M_insert(std::_List___iterator, > >>>> moab::IODebugTrack::DRange const&)': > >>>> > >>>> > IODebugTrack.cpp:(.text.___ZNSt4listIN4moab12IODebugTrack__6DRangeESaIS2_EE9_M___insertESt14_List_iteratorIS2___ERKS2_[std::list >>>> std::allocator > >>>>> ::_M_insert(std::_List___iterator, > >>>> > >>>> moab::IODebugTrack::DRange const&)]+0x3a): undefined reference to > >>>> > >>>> `std::__detail::_List_node___base::_M_hook(std::__detail::___List_node_base*)' > >>>> > >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In > >>>> function > >>>> > >>>> `__gnu_cxx::new_allocator > >>>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, > >>>> unsigned long)': > >>>> > >>>> > IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE10deallocateEPS5_m[__gnu___cxx::new_allocator > >>>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, > >>>> unsigned long)]+0x1c): undefined reference to > >>>> `operator > >>>> delete(void*)' > >>>> > >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In > >>>> function > >>>> > >>>> `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__allocate(unsigned > >>>> long, void const*)': > >>>> > >>>> > IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned > >>>> > >>>> long, void const*)]+0x2c): undefined reference to > >>>> `std::__throw_bad_alloc()' > >>>> > >>>> > IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned > >>>> > >>>> long, void const*)]+0x45): undefined reference to `operator > >>>> new(unsigned long)' > >>>> > >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In > >>>> function > >>>> > >>>> `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__deallocate(moab::IODebugTrack:__:DRange*, > >>>> unsigned > >>>> long)': > >>>> > >>>> > IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE10deallocateEPS3_m[____gnu_cxx::new_allocator::__deallocate(moab::IODebugTrack:__:DRange*, > >>>> > >>>> unsigned long)]+0x1c): undefined reference to `operator > >>>> delete(void*)' > >>>> > >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In > >>>> function > >>>> > >>>> `__gnu_cxx::new_allocator > >>>>> ::allocate(unsigned long, void const*)': > >>>> > >>>> > IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator > >>>> > >>>> >::allocate(unsigned long, void const*)]+0x2c): undefined > >>>> reference to `std::__throw_bad_alloc()' > >>>> > >>>> > IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator > >>>> > >>>> >::allocate(unsigned long, void const*)]+0x46): undefined > >>>> reference to `operator new(unsigned long)' > >>>> > >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o):(.eh_frame+__0x24b): > >>>> undefined reference to > >>>> `__gxx_personality_v0' > >>>> > >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In > >>>> function > >>>> `moab::operator<<(std::basic___ostream >>>> std::char_traits >&, moab::OrientedBox const&)': > >>>> > >>>> OrientedBox.cpp:(.text+0x97): undefined reference to > >>>> `std::basic_ostream >& > >>>> std::operator<< > >>>> >(std::basic_ostream >>>> std::char_traits >&, char const*)' > >>>> OrientedBox.cpp:(.text+0xaf): undefined reference to > >>>> `std::basic_ostream >& > >>>> std::operator<< > >>>> >(std::basic_ostream >>>> std::char_traits >&, char const*)' > >>>> OrientedBox.cpp:(.text+0xbc): undefined reference to > >>>> `std::basic_ostream > >>>> >::operator<<(double)' > >>>> OrientedBox.cpp:(.text+0xc9): undefined reference to > >>>> `std::basic_ostream >& > >>>> std::operator<< > >>>> >(std::basic_ostream >>>> std::char_traits >&, char const*)' > >>>> OrientedBox.cpp:(.text+0xe1): undefined reference to > >>>> `std::basic_ostream >& > >>>> std::operator<< > >>>> >(std::basic_ostream >>>> std::char_traits >&, char const*)' > >>>> OrientedBox.cpp:(.text+0xee): undefined reference to > >>>> `std::basic_ostream > >>>> >::operator<<(double)' > >>>> OrientedBox.cpp:(.text+0xfb): undefined reference to > >>>> `std::basic_ostream >& > >>>> std::operator<< > >>>> >(std::basic_ostream >>>> std::char_traits >&, char const*)' > >>>> OrientedBox.cpp:(.text+0x113): undefined reference to > >>>> `std::basic_ostream >& > >>>> std::operator<< > >>>>> (std::basic_ostream >&, char const*)' > >>>> OrientedBox.cpp:(.text+0x120): undefined reference to > >>>> `std::basic_ostream > >>>> >::operator<<(double)' > >>>> > >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In > >>>> function > >>>> `__static_initialization_and___destruction_0(int, int)': > >>>> OrientedBox.cpp:(.text+0x3aaf)__: undefined reference to > >>>> `std::ios_base::Init::Init()' > >>>> OrientedBox.cpp:(.text+0x3ab4)__: undefined reference to > >>>> `std::ios_base::Init::~Init()' > >>>> > >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In > >>>> function `moab::ErrorCode > >>>> moab::EigenDecomp(moab::Matrix3 > >>>> const&, double*, moab::CartVect*)': > >>>> > >>>> > OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode > >>>> moab::EigenDecomp(moab::Matrix3 > >>>> const&, double*, moab::CartVect*)]+0xb7f): > >>>> > >>>> undefined > >>>> reference to `std::cerr' > >>>> > >>>> > OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode > >>>> moab::EigenDecomp(moab::Matrix3 > >>>> const&, double*, moab::CartVect*)]+0xb84): > >>>> > >>>> undefined > >>>> reference to `std::basic_ostream >& > >>>> std::operator<< > >>>> >(std::basic_ostream >&, char > >>>> const*)' > >>>> > >>>> > OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode > >>>> moab::EigenDecomp(moab::Matrix3 > >>>> const&, double*, moab::CartVect*)]+0xb89): > >>>> > >>>> undefined > >>>> reference to `std::basic_ostream >& > >>>> std::endl > >>>> >(std::basic_ostream >&)' > >>>> > >>>> > OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode > >>>> moab::EigenDecomp(moab::Matrix3 > >>>> const&, double*, moab::CartVect*)]+0xb91): > >>>> undefined > >>>> reference to `std::basic_ostream > >>>>> ::operator<<(std::basic___ostream >>>> > >>>> std::char_traits >& (*)(std::basic_ostream >>>> std::char_traits >&))' > >>>> > >>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o):(.eh_frame+__0x22f): > >>>> undefined reference to > >>>> > >>>> `__gxx_personality_v0' > >>>> collect2: ld returned 1 exit status > >>>> make: *** [nek5000] Error 1 > >>>> > >>>> Thanks, > >>>> Ami > >>>> > >>>> > >>>> _________________________________________________ > >>>> Nek5000-users mailing list > >>>> Nek5000-users at lists.mcs.anl.__gov > >>>> > >>>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > >>>> > >>>> > >>>> > >>>> -- > >>>> ==============================__==============================__==== > >>>> > >>>> "You will keep in perfect peace him whose mind is > >>>> steadfast, because he trusts in you." Isaiah 26:3 > >>>> > >>>> Tim Tautges Argonne National Laboratory > >>>> (tautges at mcs.anl.gov ) > >>>> (telecommuting from UW-Madison) > >>>> phone (gvoice): (608) 354-1459 1500 > >>>> Engineering Dr. > >>>> fax: (608) 263-4499 > >>>> Madison, WI 53706 > >>>> > >>>> _________________________________________________ > >>>> Nek5000-users mailing list > >>>> Nek5000-users at lists.mcs.anl.__gov > >>>> > >>>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> _______________________________________________ > >>>> Nek5000-users mailing list > >>>> Nek5000-users at lists.mcs.anl.gov > >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >>>> > >>> > >>> -- > >>> ================================================================ > >>> "You will keep in perfect peace him whose mind is > >>> steadfast, because he trusts in you." Isaiah 26:3 > >>> > >>> Tim Tautges Argonne National Laboratory > >>> (tautges at mcs.anl.gov) (telecommuting from UW-Madison) > >>> phone (gvoice): (608) 354-1459 1500 Engineering Dr. > >>> fax: (608) 263-4499 Madison, WI 53706 > >>> > >>> _______________________________________________ > >>> Nek5000-users mailing list > >>> Nek5000-users at lists.mcs.anl.gov > >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >> > >> > >> > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users at lists.mcs.anl.gov > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >> > > > > -- > ================================================================ > "You will keep in perfect peace him whose mind is > steadfast, because he trusts in you." Isaiah 26:3 > > Tim Tautges Argonne National Laboratory > (tautges at mcs.anl.gov) (telecommuting from UW-Madison) > phone (gvoice): (608) 354-1459 1500 Engineering Dr. > fax: (608) 263-4499 Madison, WI 53706 > > -- ================================================================ "You will keep in perfect peace him whose mind is steadfast, because he trusts in you." Isaiah 26:3 Tim Tautges Argonne National Laboratory (tautges at mcs.anl.gov) (telecommuting from UW-Madison) phone (gvoice): (608) 354-1459 1500 Engineering Dr. fax: (608) 263-4499 Madison, WI 53706 From nek5000-users at lists.mcs.anl.gov Thu Sep 12 13:43:25 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 12 Sep 2013 14:43:25 -0400 Subject: [Nek5000-users] Running MOAB example In-Reply-To: References: <192817286.8839645.1378919428460.JavaMail.root@mcs.anl.gov> Message-ID: Hi All, After fixing MOAB, I successully compiled MOAB example but when I tried ./nek pipe, it gave me this error mv: cannot stat `pipe.log': No such file or directory ./nek5000: error while loading shared libraries: libhdf5.so.8: cannot open shared object file: No such file or directory real 0m0.001s user 0m0.000s sys 0m0.000s can any one tell me what is the problem? FYI, I am using hdf5-1.8.11 with zlib-1.2.5 and szip-2.1. Thanks, Ami On Wed, Sep 11, 2013 at 1:30 PM, wrote: > > > On 09/11/2013 12:10 PM, Iulian Grindeanu wrote: > >> >> >> ------------------------------**------------------------------** >> ------------------------------**------------------------------ >> >> >> Aha, good catch. >> >> Iulian, could you backport the imesh_freememory function? Thanks. >> >> Hello, >> The Version 4.6 was released on February 11. The link to the tar ball is >> in the web page. >> http://trac.mcs.anl.gov/**projects/ITAPS/wiki/MOAB >> >> http://ftp.mcs.anl.gov/pub/**fathom/moab-4.6.0.tar.gz >> (so this is the official release 4.6) >> >> The current Version4.6 branch, in the git repository, already has the >> free memory function backported. >> That tarball is updated nightly, and you can get it from this link (on >> the moab wiki page too) >> >> http://ftp.mcs.anl.gov/pub/**fathom/moab-4.6-nightly.tar.gz >> >> Is this what they need? >> >> > Ok, yes, that's what they need, thanks. > > - tim > > > Thanks, >> Iulian >> >> - tim >> >> On 09/11/2013 11:33 AM, Vijay S. Mahadevan wrote: >> > The linker error is because of your version mismatch. You need to >> > update your moab to the latest version. I see you are using v4.6 >> now. >> > You should be able to use the dev version from >> > https://bitbucket.org/**fathomteam/moabwith git or download the newer >> > patch from https://trac.mcs.anl.gov/**projects/ITAPS/wiki/MOAB >> . >> > >> > Tim, can we create a new patched version of the release for >> download. >> > I spoke to Rajeev about this some time back but we need to decide >> what >> > fixes to backport. >> > >> > Vijay >> > >> > On Wed, Sep 11, 2013 at 11:20 AM, > gov > wrote: >> >> >> >> Yes , I am using gnu, and whwen I add USR_LFLAGS="-lmpi_cxx >> -lstdc++, >> >> I get this, >> >> makenek - automatic build tool for Nek5000 >> >> generating makefile ... >> >> mpif77 -c -O2 -fdefault-real-8 -x f77-cpp-input -fcray-pointer >> -DMOAB >> >> -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG >> >> -I/home/amirreza/nek5_svn/**amirreza_test/examples/moab >> >> -I/home/amirreza/nek5_svn/**trunk/nek -I./ >> >> /home/amirreza/nek5_svn/**amirreza_test/examples/moab/**pipe.f >> >> -I/home/amirreza/nek5_svn/**trunk/nek/3rd_party >> >> -I/home/amirreza/Amirreza/**moab-4.6.0/gcc/include -o obj/pipe.o >> >> mpif77 -o nek5000 obj/pipe.o obj/drive.o obj/drive1.o >> obj/drive2.o >> >> obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o >> >> obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o >> >> obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o >> >> obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o >> >> obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o >> obj/math.o >> >> obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o >> >> obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o >> obj/hsmg.o >> >> obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o >> obj/navier6.o >> >> obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o >> obj/byte.o >> >> obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o >> >> obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o >> >> obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o >> >> obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o >> obj/imeshutil.o >> >> obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o >> obj/jl_sort.o >> >> obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o >> >> obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o >> >> obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o >> obj/jl_obbox.o >> >> obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o >> obj/jl_findpts_el_2.o >> >> obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o >> >> -L/home/amirreza/Amirreza/**netcdf-4.1.3/gcc/lib >> >> -L/home/amirreza/Amirreza/**zlib-1.2.5/gcc/lib >> >> -L/home/amirreza/Amirreza/**szip-2.1/gcc/lib >> >> -L/home/amirreza/Amirreza/**hdf5-1.8.11/lib >> >> -L/home/amirreza/Amirreza/**moab-4.6.0/gcc/lib >> >> -L/home/amirreza/Amirreza/**moab-4.6.0/gcc/lib -liMesh -lMOAB >> -lnetcdf -lhdf5 >> >> -lsz -lm -lmpi_cxx -lstdc++ >> >> obj/moab.o: In function `nekmoab_intbc_': >> >> moab.f:(.text+0xe9d): undefined reference to `imesh_freememory_' >> >> moab.f:(.text+0xece): undefined reference to `imesh_freememory_' >> >> moab.f:(.text+0xee4): undefined reference to `imesh_freememory_' >> >> moab.f:(.text+0xf05): undefined reference to `imesh_freememory_' >> >> obj/moab.o: In function `nekmoab_bc_': >> >> moab.f:(.text+0x1306): undefined reference to `imesh_freememory_' >> >> >> >> collect2: ld returned 1 exit status >> >> make: *** [nek5000] Error 1 >> >> >> >> Thanks, >> >> Ami >> >> >> >> >> >> On Wed, Sep 11, 2013 at 12:05 PM, > gov > wrote: >> >>> >> >>> It depends which compiler you're using. Are you using gnu? >> >>> >> >>> Please send complete compile output. >> >>> >> >>> - tim >> >>> >> >>> >> >>> On 09/11/2013 10:11 AM, nek5000-users at lists.mcs.anl.**govwrote: >> >>>> >> >>>> Thanks for your answer, to make sure I have added libraries to >> makenek >> >>>> ''USR_LFLAGS="-lmpi_cxx -lstdc++" which I'm >> >>>> getting same error,so you mean I need to add appropriate >> fortran library >> >>>> to USR_LFLAGS? >> >>>> >> >>>> Thanks, >> >>>> Ami >> >>>> >> >>>> >> >>>> On Wed, Sep 11, 2013 at 10:47 AM, > **gov >> >>>> >> >> wrote: >> >>>> >> >>>> Hi Ami, >> >>>> That's the C++ runtime. You have two options: >> >>>> 1. Link with the C++ compiler; in this case, you'll have to >> >>>> explicitly add the fortran runtime libraries to the link >> >>>> statement, which is most easily done by adding it to >> USR_LFLAGS in >> >>>> makenek. Compiler documents often tell you which >> >>>> libraries implement the fortran runtime, usually in a >> section about >> >>>> inter-language linking. >> >>>> >> >>>> 2. Add the C++ std libs to USR_LFLAGS. The >> trunk/nek/makenek file >> >>>> has a few examples of this method for >> >>>> gnu/intel/pgi. Sometimes, like on BG/x, it can be >> difficult to >> >>>> figure out what all comprises the C++ runtime, which >> >>>> is why I list 1. above. >> >>>> >> >>>> - tim >> >>>> >> >>>> >> >>>> On 09/11/2013 09:31 AM, nek5000-users at lists.mcs.anl.__** >> gov >> >>>> > >> wrote: >> >>>> >> >>>> Hello Neks, >> >>>> >> >>>> I am trying to run MOAB example with nek5000, but all >> the time >> >>>> which I am running, it gives me set of undefined >> >>>> reference error. I put an error with last part of my >> ./makenek >> >>>> pipe log below. >> >>>> What is wrong with my work? >> >>>> >> >>>> IODebugTrack.cpp:(.text+0xb74)**__: undefined >> reference to >> >>>> `std::basic_ostream >& >> >>>> >> >>>> std::operator<< >> >>>>> (std::basic_ostream >&, char >> const*)' >> >>>> IODebugTrack.cpp:(.text+0xb7f)**__: undefined >> reference to >> >>>> `std::basic_ostream >> >>>> >::operator<<(unsigned long)' >> >>>> IODebugTrack.cpp:(.text+0xb8c)**__: undefined >> reference to >> >>>> `std::basic_ostream >& >> >>>> >> >>>> std::operator<< >> >>>>> (std::basic_ostream >&, char >> const*)' >> >>>> IODebugTrack.cpp:(.text+0xb97)**__: undefined >> reference to >> >>>> `std::basic_ostream >> >>>> >::operator<<(unsigned long)' >> >>>> IODebugTrack.cpp:(.text+0xbd3)**__: undefined >> reference to >> >>>> `std::basic_ostream >& >> >>>> >> >>>> std::operator<< >> >>>>> (std::basic_ostream >&, char >> const*)' >> >>>> IODebugTrack.cpp:(.text+0xbde)**__: undefined >> reference to >> >>>> `std::basic_ostream >> >>>> >::operator<<(unsigned long)' >> >>>> IODebugTrack.cpp:(.text+0xbeb)**__: undefined >> reference to >> >>>> `std::basic_ostream >& >> >>>> >> >>>> std::operator<< >> >>>>> (std::basic_ostream >&, char >> const*)' >> >>>> IODebugTrack.cpp:(.text+0xbf6)**__: undefined >> reference to >> >>>> `std::basic_ostream >> >>>> >::operator<<(unsigned long)' >> >>>> IODebugTrack.cpp:(.text+0xc03)**__: undefined >> reference to >> >>>> `std::basic_ostream >& >> >>>> >> >>>> std::operator<< >> >>>>> (std::basic_ostream >&, char >> const*)' >> >>>> IODebugTrack.cpp:(.text+0xc0e)**__: undefined >> reference to >> >>>> `std::basic_ostream >> >>>> >::operator<<(unsigned long)' >> >>>> IODebugTrack.cpp:(.text+0xc1b)**__: undefined >> reference to >> >>>> `std::basic_ostream >& >> >>>> >> >>>> std::operator<< >> >>>>> (std::basic_ostream >&, char >> const*)' >> >>>> IODebugTrack.cpp:(.text+0xc26)**__: undefined >> reference to >> >>>> `std::basic_ostream >> >>>> >::operator<<(unsigned long)' >> >>>> IODebugTrack.cpp:(.text+0xc33)**__: undefined >> reference to >> >>>> `std::basic_ostream >& >> >>>> >> >>>> std::operator<< >> >>>>> (std::basic_ostream >&, char >> const*)' >> >>>> IODebugTrack.cpp:(.text+0xc38)**__: undefined >> reference to >> >>>> `std::basic_ostream >& >> >>>> >> >>>> std::endl >> >(std::basic_ostream> >>>> std::char_traits >&)' >> >>>> IODebugTrack.cpp:(.text+0xc40)**__: undefined >> reference to >> >>>> `std::basic_ostream >> >>>> >::operator<<(std::basic___**ostream> std::char_traits >> >>>>> & (*)(std::basic_ostream> >>>> std::char_traits >&))' >> >>>> IODebugTrack.cpp:(.text+0xc50)**__: undefined >> reference to >> >>>> `std::basic_ostream >> >>>> >::flush()' >> >>>> >> >>>> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**IODebugTrack.o): >> In >> >>>> function >> >>>> `moab::IODebugTrack::all___**reduce()': >> >>>> IODebugTrack.cpp:(.text+0xd08)**__: undefined >> reference to >> >>>> `MPI_Comm_size' >> >>>> IODebugTrack.cpp:(.text+0xdfe)**__: undefined >> reference to >> >>>> `MPI_Gather' >> >>>> IODebugTrack.cpp:(.text+__**0x1080): undefined >> reference to >> >>>> `MPI_Gatherv' >> >>>> >> >>>> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**IODebugTrack.o): >> In >> >>>> function >> >>>> `__static_initialization_and__**_destruction_0(int, >> int)': >> >>>> IODebugTrack.cpp:(.text+__**0x1221): undefined >> reference to >> >>>> `std::ios_base::Init::Init()' >> >>>> IODebugTrack.cpp:(.text+__**0x1226): undefined >> reference to >> >>>> `std::ios_base::Init::~Init()' >> >>>> >> >>>> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**IODebugTrack.o): >> In >> >>>> function >> >>>> `std::list> >>>> std::allocator >> >>>>> ::_M_insert(std::_List___**iterator> _DRange>, >> >>>> moab::IODebugTrack::DRange const&)': >> >>>> >> >>>> >> IODebugTrack.cpp:(.text.___**ZNSt4listIN4moab12IODebugTrack** >> __6DRangeESaIS2_EE9_M___**insertESt14_List_iteratorIS2__** >> _ERKS2_[std::list> >>>> std::allocator >> >>>>> ::_M_insert(std::_List___**iterator> _DRange>, >> >>>> >> >>>> moab::IODebugTrack::DRange const&)]+0x3a): undefined >> reference to >> >>>> >> >>>> `std::__detail::_List_node___**base::_M_hook(std::__detail::_** >> __List_node_base*)' >> >>>> >> >>>> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**IODebugTrack.o): >> In >> >>>> function >> >>>> >> >>>> `__gnu_cxx::new_allocator> IODebugTrack::DRange> >> >>>> >::deallocate(std::_List_node<** >> __moab::IODebugTrack::DRange>***, >> >>>> unsigned long)': >> >>>> >> >>>> >> IODebugTrack.cpp:(.text._ZN9__**__gnu_cxx13new_allocatorISt10_** >> __List___**nodeIN4moab12IODebugTrack6DRan**__geEEE10deallocateEPS5_m[__** >> gnu___cxx::new_allocator> IODebugTrack::__DRange> >> >>>> >::deallocate(std::_List_node<** >> __moab::IODebugTrack::DRange>***, >> >>>> unsigned long)]+0x1c): undefined reference to >> >>>> `operator >> >>>> delete(void*)' >> >>>> >> >>>> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**IODebugTrack.o): >> In >> >>>> function >> >>>> >> >>>> `__gnu_cxx::new_allocator<__**moab::IODebugTrack::DRange>::_** >> _allocate(unsigned >> >>>> long, void const*)': >> >>>> >> >>>> >> IODebugTrack.cpp:(.text._ZN9__**__gnu_cxx13new___** >> allocatorIN4moab12IODebugTrack**__6DRangeEE8allocateEmPKv[__** >> gnu___cxx::new_allocator::__** >> allocate(unsigned >> >>>> >> >>>> long, void const*)]+0x2c): undefined reference to >> >>>> `std::__throw_bad_alloc()' >> >>>> >> >>>> >> IODebugTrack.cpp:(.text._ZN9__**__gnu_cxx13new___** >> allocatorIN4moab12IODebugTrack**__6DRangeEE8allocateEmPKv[__** >> gnu___cxx::new_allocator::__** >> allocate(unsigned >> >>>> >> >>>> long, void const*)]+0x45): undefined reference to >> `operator >> >>>> new(unsigned long)' >> >>>> >> >>>> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**IODebugTrack.o): >> In >> >>>> function >> >>>> >> >>>> `__gnu_cxx::new_allocator<__**moab::IODebugTrack::DRange>::_** >> _deallocate(moab::**IODebugTrack:__:DRange*, >> >>>> unsigned >> >>>> long)': >> >>>> >> >>>> >> IODebugTrack.cpp:(.text._ZN9__**__gnu_cxx13new___** >> allocatorIN4moab12IODebugTrack**__6DRangeEE10deallocateEPS3_m[** >> ____gnu_cxx::new_allocator<**moab::__IODebugTrack::DRange>:** >> :__deallocate(moab::**IODebugTrack:__:DRange*, >> >>>> >> >>>> unsigned long)]+0x1c): undefined reference to `operator >> >>>> delete(void*)' >> >>>> >> >>>> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**IODebugTrack.o): >> In >> >>>> function >> >>>> >> >>>> `__gnu_cxx::new_allocator> IODebugTrack::DRange> >> >>>>> ::allocate(unsigned long, void const*)': >> >>>> >> >>>> >> IODebugTrack.cpp:(.text._ZN9__**__gnu_cxx13new_allocatorISt10_** >> __List___**nodeIN4moab12IODebugTrack6DRan**__geEEE8allocateEmPKv[__gnu_** >> cxx:__:new_allocator >> >>>> >> >>>> >::allocate(unsigned long, void const*)]+0x2c): >> undefined >> >>>> reference to `std::__throw_bad_alloc()' >> >>>> >> >>>> >> IODebugTrack.cpp:(.text._ZN9__**__gnu_cxx13new_allocatorISt10_** >> __List___**nodeIN4moab12IODebugTrack6DRan**__geEEE8allocateEmPKv[__gnu_** >> cxx:__:new_allocator >> >>>> >> >>>> >::allocate(unsigned long, void const*)]+0x46): >> undefined >> >>>> reference to `operator new(unsigned long)' >> >>>> >> >>>> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__** >> IODebugTrack.o):(.eh_frame+__**0x24b): >> >>>> undefined reference to >> >>>> `__gxx_personality_v0' >> >>>> >> >>>> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**OrientedBox.o): >> In >> >>>> function >> >>>> `moab::operator<<(std::basic__**_ostream> >>>> std::char_traits >&, moab::OrientedBox const&)': >> >>>> >> >>>> OrientedBox.cpp:(.text+0x97): undefined reference to >> >>>> `std::basic_ostream >& >> >>>> std::operator<< >> >>>> >(std::basic_ostream> >>>> std::char_traits >&, char const*)' >> >>>> OrientedBox.cpp:(.text+0xaf): undefined reference to >> >>>> `std::basic_ostream >& >> >>>> std::operator<< >> >>>> >(std::basic_ostream> >>>> std::char_traits >&, char const*)' >> >>>> OrientedBox.cpp:(.text+0xbc): undefined reference to >> >>>> `std::basic_ostream >> >>>> >::operator<<(double)' >> >>>> OrientedBox.cpp:(.text+0xc9): undefined reference to >> >>>> `std::basic_ostream >& >> >>>> std::operator<< >> >>>> >(std::basic_ostream> >>>> std::char_traits >&, char const*)' >> >>>> OrientedBox.cpp:(.text+0xe1): undefined reference to >> >>>> `std::basic_ostream >& >> >>>> std::operator<< >> >>>> >(std::basic_ostream> >>>> std::char_traits >&, char const*)' >> >>>> OrientedBox.cpp:(.text+0xee): undefined reference to >> >>>> `std::basic_ostream >> >>>> >::operator<<(double)' >> >>>> OrientedBox.cpp:(.text+0xfb): undefined reference to >> >>>> `std::basic_ostream >& >> >>>> std::operator<< >> >>>> >(std::basic_ostream> >>>> std::char_traits >&, char const*)' >> >>>> OrientedBox.cpp:(.text+0x113): undefined reference to >> >>>> `std::basic_ostream >& >> >>>> std::operator<< >> >>>>> (std::basic_ostream >&, char >> const*)' >> >>>> OrientedBox.cpp:(.text+0x120): undefined reference to >> >>>> `std::basic_ostream >> >>>> >::operator<<(double)' >> >>>> >> >>>> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**OrientedBox.o): >> In >> >>>> function >> >>>> `__static_initialization_and__**_destruction_0(int, >> int)': >> >>>> OrientedBox.cpp:(.text+0x3aaf)**__: undefined >> reference to >> >>>> `std::ios_base::Init::Init()' >> >>>> OrientedBox.cpp:(.text+0x3ab4)**__: undefined >> reference to >> >>>> `std::ios_base::Init::~Init()' >> >>>> >> >>>> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__**OrientedBox.o): >> In >> >>>> function `moab::ErrorCode >> >>>> moab::EigenDecomp> moab::CartVect>(moab::Matrix3 >> >>>> const&, double*, moab::CartVect*)': >> >>>> >> >>>> >> OrientedBox.cpp:(.text.___**ZN4moab11EigenDecompINS___** >> 7Matrix3ENS_8CartVectEEENS___**9ErrorCodeERKT_PdPT0_[moab::__**ErrorCode >> >>>> moab::EigenDecomp> moab::CartVect>(moab::Matrix3 >> >>>> const&, double*, moab::CartVect*)]+0xb7f): >> >>>> >> >>>> undefined >> >>>> reference to `std::cerr' >> >>>> >> >>>> >> OrientedBox.cpp:(.text.___**ZN4moab11EigenDecompINS___** >> 7Matrix3ENS_8CartVectEEENS___**9ErrorCodeERKT_PdPT0_[moab::__**ErrorCode >> >>>> moab::EigenDecomp> moab::CartVect>(moab::Matrix3 >> >>>> const&, double*, moab::CartVect*)]+0xb84): >> >>>> >> >>>> undefined >> >>>> reference to `std::basic_ostream> std::char_traits >& >> >>>> std::operator<< >> >>>> >(std::basic_ostream >> >&, char >> >>>> const*)' >> >>>> >> >>>> >> OrientedBox.cpp:(.text.___**ZN4moab11EigenDecompINS___** >> 7Matrix3ENS_8CartVectEEENS___**9ErrorCodeERKT_PdPT0_[moab::__**ErrorCode >> >>>> moab::EigenDecomp> moab::CartVect>(moab::Matrix3 >> >>>> const&, double*, moab::CartVect*)]+0xb89): >> >>>> >> >>>> undefined >> >>>> reference to `std::basic_ostream> std::char_traits >& >> >>>> std::endl >> >>>> >(std::basic_ostream >> >&)' >> >>>> >> >>>> >> OrientedBox.cpp:(.text.___**ZN4moab11EigenDecompINS___** >> 7Matrix3ENS_8CartVectEEENS___**9ErrorCodeERKT_PdPT0_[moab::__**ErrorCode >> >>>> moab::EigenDecomp> moab::CartVect>(moab::Matrix3 >> >>>> const&, double*, moab::CartVect*)]+0xb91): >> >>>> undefined >> >>>> reference to `std::basic_ostream> std::char_traits >> >>>>> ::operator<<(std::basic___**ostream> >>>> >> >>>> std::char_traits >& (*)(std::basic_ostream> >>>> std::char_traits >&))' >> >>>> >> >>>> /home/amirreza/Amirreza/moab-_**_4.6.0/gcc/lib/libMOAB.a(__** >> OrientedBox.o):(.eh_frame+__**0x22f): >> >>>> undefined reference to >> >>>> >> >>>> `__gxx_personality_v0' >> >>>> collect2: ld returned 1 exit status >> >>>> make: *** [nek5000] Error 1 >> >>>> >> >>>> Thanks, >> >>>> Ami >> >>>> >> >>>> >> >>>> ______________________________**___________________ >> >>>> Nek5000-users mailing list >> >>>> Nek5000-users at lists.mcs.anl.__**gov >> >>>> >> > >> >>>> https://lists.mcs.anl.gov/__** >> mailman/listinfo/nek5000-users >> >>>> > mailman/listinfo/nek5000-users >> **> >> >>>> >> >>>> >> >>>> -- >> >>>> ==============================** >> __============================**==__==== >> >>>> >> >>>> "You will keep in perfect peace him whose mind is >> >>>> steadfast, because he trusts in you." >> Isaiah 26:3 >> >>>> >> >>>> Tim Tautges Argonne National >> Laboratory >> >>>> (tautges at mcs.anl.gov > >) >> >>>> (telecommuting from UW-Madison) >> >>>> phone (gvoice): (608) 354-1459 1500 >> >>>> Engineering Dr. >> >>>> fax: (608) 263-4499 >> >>>> Madison, WI 53706 >> >>>> >> >>>> ______________________________**___________________ >> >>>> Nek5000-users mailing list >> >>>> Nek5000-users at lists.mcs.anl.__**gov >> >>>> >> > >> >>>> https://lists.mcs.anl.gov/__** >> mailman/listinfo/nek5000-users >> >>>> >> **> >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> ______________________________**_________________ >> >>>> Nek5000-users mailing list >> >>>> Nek5000-users at lists.mcs.anl.**gov >> >>>> https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users >> >>>> >> >>> >> >>> -- >> >>> ==============================**==============================** >> ==== >> >>> "You will keep in perfect peace him whose mind is >> >>> steadfast, because he trusts in you." Isaiah >> 26:3 >> >>> >> >>> Tim Tautges Argonne National Laboratory >> >>> (tautges at mcs.anl.gov) (telecommuting from >> UW-Madison) >> >>> phone (gvoice): (608) 354-1459 1500 Engineering Dr. >> >>> fax: (608) 263-4499 Madison, WI 53706 >> >>> >> >>> ______________________________**_________________ >> >>> Nek5000-users mailing list >> >>> Nek5000-users at lists.mcs.anl.**gov >> >>> https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users >> >> >> >> >> >> >> >> ______________________________**_________________ >> >> Nek5000-users mailing list >> >> Nek5000-users at lists.mcs.anl.**gov >> >> https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users >> >> >> > >> >> -- >> ==============================**==============================**==== >> "You will keep in perfect peace him whose mind is >> steadfast, because he trusts in you." Isaiah 26:3 >> >> Tim Tautges Argonne National Laboratory >> (tautges at mcs.anl.gov) (telecommuting from UW-Madison) >> phone (gvoice): (608) 354-1459 1500 Engineering Dr. >> fax: (608) 263-4499 Madison, WI 53706 >> >> >> > -- > ==============================**==============================**==== > "You will keep in perfect peace him whose mind is > steadfast, because he trusts in you." Isaiah 26:3 > > Tim Tautges Argonne National Laboratory > (tautges at mcs.anl.gov) (telecommuting from UW-Madison) > phone (gvoice): (608) 354-1459 1500 Engineering Dr. > fax: (608) 263-4499 Madison, WI 53706 > > ______________________________**_________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.**gov > https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Sep 12 13:49:15 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 12 Sep 2013 13:49:15 -0500 Subject: [Nek5000-users] Running MOAB example In-Reply-To: References: <192817286.8839645.1378919428460.JavaMail.root@mcs.anl.gov> Message-ID: If you HDF5 and NetCDF are configured as shared libraries, make sure their library paths are included in LD_LIBRARY_PATH. e.g., export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/amirreza/Amirreza/hdf5-1.8.11/lib Also check ldd ./nek5000 to make sure that all the necessary libraries are being resolved correctly before attempting to run the code again. Vijay On Thu, Sep 12, 2013 at 1:43 PM, wrote: > Hi All, > > After fixing MOAB, I successully compiled MOAB example but when I tried > ./nek pipe, it gave me this error > > mv: cannot stat `pipe.log': No such file or directory > ./nek5000: error while loading shared libraries: libhdf5.so.8: cannot open > shared object file: No such file or directory > > real 0m0.001s > user 0m0.000s > sys 0m0.000s > > can any one tell me what is the problem? FYI, I am using hdf5-1.8.11 with > zlib-1.2.5 and szip-2.1. > > Thanks, > Ami > > > On Wed, Sep 11, 2013 at 1:30 PM, wrote: >> >> >> >> On 09/11/2013 12:10 PM, Iulian Grindeanu wrote: >>> >>> >>> >>> >>> ------------------------------------------------------------------------------------------------------------------------ >>> >>> >>> Aha, good catch. >>> >>> Iulian, could you backport the imesh_freememory function? Thanks. >>> >>> Hello, >>> The Version 4.6 was released on February 11. The link to the tar ball is >>> in the web page. >>> http://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB >>> >>> http://ftp.mcs.anl.gov/pub/fathom/moab-4.6.0.tar.gz >>> (so this is the official release 4.6) >>> >>> The current Version4.6 branch, in the git repository, already has the >>> free memory function backported. >>> That tarball is updated nightly, and you can get it from this link (on >>> the moab wiki page too) >>> >>> http://ftp.mcs.anl.gov/pub/fathom/moab-4.6-nightly.tar.gz >>> >>> Is this what they need? >>> >> >> Ok, yes, that's what they need, thanks. >> >> - tim >> >> >>> Thanks, >>> Iulian >>> >>> - tim >>> >>> On 09/11/2013 11:33 AM, Vijay S. Mahadevan wrote: >>> > The linker error is because of your version mismatch. You need to >>> > update your moab to the latest version. I see you are using v4.6 >>> now. >>> > You should be able to use the dev version from >>> > https://bitbucket.org/fathomteam/moab with git or download the >>> newer >>> > patch from https://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB. >>> > >>> > Tim, can we create a new patched version of the release for >>> download. >>> > I spoke to Rajeev about this some time back but we need to decide >>> what >>> > fixes to backport. >>> > >>> > Vijay >>> > >>> > On Wed, Sep 11, 2013 at 11:20 AM, >>> wrote: >>> >> >>> >> Yes , I am using gnu, and whwen I add USR_LFLAGS="-lmpi_cxx >>> -lstdc++, >>> >> I get this, >>> >> makenek - automatic build tool for Nek5000 >>> >> generating makefile ... >>> >> mpif77 -c -O2 -fdefault-real-8 -x f77-cpp-input -fcray-pointer >>> -DMOAB >>> >> -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG >>> >> -I/home/amirreza/nek5_svn/amirreza_test/examples/moab >>> >> -I/home/amirreza/nek5_svn/trunk/nek -I./ >>> >> /home/amirreza/nek5_svn/amirreza_test/examples/moab/pipe.f >>> >> -I/home/amirreza/nek5_svn/trunk/nek/3rd_party >>> >> -I/home/amirreza/Amirreza/moab-4.6.0/gcc/include -o obj/pipe.o >>> >> mpif77 -o nek5000 obj/pipe.o obj/drive.o obj/drive1.o >>> obj/drive2.o >>> >> obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o >>> >> obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o >>> >> obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o >>> obj/navier2.o >>> >> obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o >>> obj/map2.o >>> >> obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o >>> obj/math.o >>> >> obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o >>> >> obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o >>> obj/hsmg.o >>> >> obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o >>> obj/navier6.o >>> >> obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o >>> obj/byte.o >>> >> obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o >>> >> obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o >>> >> obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o >>> obj/dsygv.o >>> >> obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o >>> obj/imeshutil.o >>> >> obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o >>> obj/jl_sort.o >>> >> obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o >>> >> obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o >>> >> obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o >>> obj/jl_obbox.o >>> >> obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o >>> obj/jl_findpts_el_2.o >>> >> obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o >>> >> -L/home/amirreza/Amirreza/netcdf-4.1.3/gcc/lib >>> >> -L/home/amirreza/Amirreza/zlib-1.2.5/gcc/lib >>> >> -L/home/amirreza/Amirreza/szip-2.1/gcc/lib >>> >> -L/home/amirreza/Amirreza/hdf5-1.8.11/lib >>> >> -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib >>> >> -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib -liMesh -lMOAB >>> -lnetcdf -lhdf5 >>> >> -lsz -lm -lmpi_cxx -lstdc++ >>> >> obj/moab.o: In function `nekmoab_intbc_': >>> >> moab.f:(.text+0xe9d): undefined reference to `imesh_freememory_' >>> >> moab.f:(.text+0xece): undefined reference to `imesh_freememory_' >>> >> moab.f:(.text+0xee4): undefined reference to `imesh_freememory_' >>> >> moab.f:(.text+0xf05): undefined reference to `imesh_freememory_' >>> >> obj/moab.o: In function `nekmoab_bc_': >>> >> moab.f:(.text+0x1306): undefined reference to `imesh_freememory_' >>> >> >>> >> collect2: ld returned 1 exit status >>> >> make: *** [nek5000] Error 1 >>> >> >>> >> Thanks, >>> >> Ami >>> >> >>> >> >>> >> On Wed, Sep 11, 2013 at 12:05 PM, >>> wrote: >>> >>> >>> >>> It depends which compiler you're using. Are you using gnu? >>> >>> >>> >>> Please send complete compile output. >>> >>> >>> >>> - tim >>> >>> >>> >>> >>> >>> On 09/11/2013 10:11 AM, nek5000-users at lists.mcs.anl.gov wrote: >>> >>>> >>> >>>> Thanks for your answer, to make sure I have added libraries to >>> makenek >>> >>>> ''USR_LFLAGS="-lmpi_cxx -lstdc++" which I'm >>> >>>> getting same error,so you mean I need to add appropriate >>> fortran library >>> >>>> to USR_LFLAGS? >>> >>>> >>> >>>> Thanks, >>> >>>> Ami >>> >>>> >>> >>>> >>> >>>> On Wed, Sep 11, 2013 at 10:47 AM, >>> >> >>>> > wrote: >>> >>>> >>> >>>> Hi Ami, >>> >>>> That's the C++ runtime. You have two options: >>> >>>> 1. Link with the C++ compiler; in this case, you'll have >>> to >>> >>>> explicitly add the fortran runtime libraries to the link >>> >>>> statement, which is most easily done by adding it to >>> USR_LFLAGS in >>> >>>> makenek. Compiler documents often tell you which >>> >>>> libraries implement the fortran runtime, usually in a >>> section about >>> >>>> inter-language linking. >>> >>>> >>> >>>> 2. Add the C++ std libs to USR_LFLAGS. The >>> trunk/nek/makenek file >>> >>>> has a few examples of this method for >>> >>>> gnu/intel/pgi. Sometimes, like on BG/x, it can be >>> difficult to >>> >>>> figure out what all comprises the C++ runtime, which >>> >>>> is why I list 1. above. >>> >>>> >>> >>>> - tim >>> >>>> >>> >>>> >>> >>>> On 09/11/2013 09:31 AM, nek5000-users at lists.mcs.anl.__gov >>> >>>> wrote: >>> >>>> >>> >>>> Hello Neks, >>> >>>> >>> >>>> I am trying to run MOAB example with nek5000, but all >>> the time >>> >>>> which I am running, it gives me set of undefined >>> >>>> reference error. I put an error with last part of my >>> ./makenek >>> >>>> pipe log below. >>> >>>> What is wrong with my work? >>> >>>> >>> >>>> IODebugTrack.cpp:(.text+0xb74)__: undefined reference >>> to >>> >>>> `std::basic_ostream >& >>> >>>> >>> >>>> std::operator<< >>> >>>>> (std::basic_ostream >&, char >>> const*)' >>> >>>> IODebugTrack.cpp:(.text+0xb7f)__: undefined reference >>> to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(unsigned long)' >>> >>>> IODebugTrack.cpp:(.text+0xb8c)__: undefined reference >>> to >>> >>>> `std::basic_ostream >& >>> >>>> >>> >>>> std::operator<< >>> >>>>> (std::basic_ostream >&, char >>> const*)' >>> >>>> IODebugTrack.cpp:(.text+0xb97)__: undefined reference >>> to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(unsigned long)' >>> >>>> IODebugTrack.cpp:(.text+0xbd3)__: undefined reference >>> to >>> >>>> `std::basic_ostream >& >>> >>>> >>> >>>> std::operator<< >>> >>>>> (std::basic_ostream >&, char >>> const*)' >>> >>>> IODebugTrack.cpp:(.text+0xbde)__: undefined reference >>> to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(unsigned long)' >>> >>>> IODebugTrack.cpp:(.text+0xbeb)__: undefined reference >>> to >>> >>>> `std::basic_ostream >& >>> >>>> >>> >>>> std::operator<< >>> >>>>> (std::basic_ostream >&, char >>> const*)' >>> >>>> IODebugTrack.cpp:(.text+0xbf6)__: undefined reference >>> to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(unsigned long)' >>> >>>> IODebugTrack.cpp:(.text+0xc03)__: undefined reference >>> to >>> >>>> `std::basic_ostream >& >>> >>>> >>> >>>> std::operator<< >>> >>>>> (std::basic_ostream >&, char >>> const*)' >>> >>>> IODebugTrack.cpp:(.text+0xc0e)__: undefined reference >>> to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(unsigned long)' >>> >>>> IODebugTrack.cpp:(.text+0xc1b)__: undefined reference >>> to >>> >>>> `std::basic_ostream >& >>> >>>> >>> >>>> std::operator<< >>> >>>>> (std::basic_ostream >&, char >>> const*)' >>> >>>> IODebugTrack.cpp:(.text+0xc26)__: undefined reference >>> to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(unsigned long)' >>> >>>> IODebugTrack.cpp:(.text+0xc33)__: undefined reference >>> to >>> >>>> `std::basic_ostream >& >>> >>>> >>> >>>> std::operator<< >>> >>>>> (std::basic_ostream >&, char >>> const*)' >>> >>>> IODebugTrack.cpp:(.text+0xc38)__: undefined reference >>> to >>> >>>> `std::basic_ostream >& >>> >>>> >>> >>>> std::endl >>> >(std::basic_ostream>> >>>> std::char_traits >&)' >>> >>>> IODebugTrack.cpp:(.text+0xc40)__: undefined reference >>> to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(std::basic___ostream>> std::char_traits >>> >>>>> & (*)(std::basic_ostream>> >>>> std::char_traits >&))' >>> >>>> IODebugTrack.cpp:(.text+0xc50)__: undefined reference >>> to >>> >>>> `std::basic_ostream >>> >>>> >::flush()' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> >>>> function >>> >>>> `moab::IODebugTrack::all___reduce()': >>> >>>> IODebugTrack.cpp:(.text+0xd08)__: undefined reference >>> to >>> >>>> `MPI_Comm_size' >>> >>>> IODebugTrack.cpp:(.text+0xdfe)__: undefined reference >>> to >>> >>>> `MPI_Gather' >>> >>>> IODebugTrack.cpp:(.text+__0x1080): undefined reference >>> to >>> >>>> `MPI_Gatherv' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> >>>> function >>> >>>> `__static_initialization_and___destruction_0(int, >>> int)': >>> >>>> IODebugTrack.cpp:(.text+__0x1221): undefined reference >>> to >>> >>>> `std::ios_base::Init::Init()' >>> >>>> IODebugTrack.cpp:(.text+__0x1226): undefined reference >>> to >>> >>>> `std::ios_base::Init::~Init()' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> >>>> function >>> >>>> `std::list>> >>>> std::allocator >>> >>>>> >>> ::_M_insert(std::_List___iterator, >>> >>>> moab::IODebugTrack::DRange const&)': >>> >>>> >>> >>>> >>> >>> IODebugTrack.cpp:(.text.___ZNSt4listIN4moab12IODebugTrack__6DRangeESaIS2_EE9_M___insertESt14_List_iteratorIS2___ERKS2_[std::list>> >>>> std::allocator >>> >>>>> >>> ::_M_insert(std::_List___iterator, >>> >>>> >>> >>>> moab::IODebugTrack::DRange const&)]+0x3a): undefined >>> reference to >>> >>>> >>> >>>> >>> `std::__detail::_List_node___base::_M_hook(std::__detail::___List_node_base*)' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> >>>> function >>> >>>> >>> >>>> >>> `__gnu_cxx::new_allocator >>> >>>> >>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, >>> >>>> unsigned long)': >>> >>>> >>> >>>> >>> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE10deallocateEPS5_m[__gnu___cxx::new_allocator >>> >>>> >>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, >>> >>>> unsigned long)]+0x1c): undefined reference to >>> >>>> `operator >>> >>>> delete(void*)' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> >>>> function >>> >>>> >>> >>>> >>> `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__allocate(unsigned >>> >>>> long, void const*)': >>> >>>> >>> >>>> >>> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned >>> >>>> >>> >>>> long, void const*)]+0x2c): undefined reference to >>> >>>> `std::__throw_bad_alloc()' >>> >>>> >>> >>>> >>> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned >>> >>>> >>> >>>> long, void const*)]+0x45): undefined reference to >>> `operator >>> >>>> new(unsigned long)' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> >>>> function >>> >>>> >>> >>>> >>> `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__deallocate(moab::IODebugTrack:__:DRange*, >>> >>>> unsigned >>> >>>> long)': >>> >>>> >>> >>>> >>> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE10deallocateEPS3_m[____gnu_cxx::new_allocator::__deallocate(moab::IODebugTrack:__:DRange*, >>> >>>> >>> >>>> unsigned long)]+0x1c): undefined reference to >>> `operator >>> >>>> delete(void*)' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> >>>> function >>> >>>> >>> >>>> >>> `__gnu_cxx::new_allocator >>> >>>>> ::allocate(unsigned long, void const*)': >>> >>>> >>> >>>> >>> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator >>> >>>> >>> >>>> >::allocate(unsigned long, void const*)]+0x2c): >>> undefined >>> >>>> reference to `std::__throw_bad_alloc()' >>> >>>> >>> >>>> >>> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator >>> >>>> >>> >>>> >::allocate(unsigned long, void const*)]+0x46): >>> undefined >>> >>>> reference to `operator new(unsigned long)' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o):(.eh_frame+__0x24b): >>> >>>> undefined reference to >>> >>>> `__gxx_personality_v0' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In >>> >>>> function >>> >>>> `moab::operator<<(std::basic___ostream>> >>>> std::char_traits >&, moab::OrientedBox const&)': >>> >>>> >>> >>>> OrientedBox.cpp:(.text+0x97): undefined reference to >>> >>>> `std::basic_ostream >& >>> >>>> std::operator<< >>> >>>> >(std::basic_ostream>> >>>> std::char_traits >&, char const*)' >>> >>>> OrientedBox.cpp:(.text+0xaf): undefined reference to >>> >>>> `std::basic_ostream >& >>> >>>> std::operator<< >>> >>>> >(std::basic_ostream>> >>>> std::char_traits >&, char const*)' >>> >>>> OrientedBox.cpp:(.text+0xbc): undefined reference to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(double)' >>> >>>> OrientedBox.cpp:(.text+0xc9): undefined reference to >>> >>>> `std::basic_ostream >& >>> >>>> std::operator<< >>> >>>> >(std::basic_ostream>> >>>> std::char_traits >&, char const*)' >>> >>>> OrientedBox.cpp:(.text+0xe1): undefined reference to >>> >>>> `std::basic_ostream >& >>> >>>> std::operator<< >>> >>>> >(std::basic_ostream>> >>>> std::char_traits >&, char const*)' >>> >>>> OrientedBox.cpp:(.text+0xee): undefined reference to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(double)' >>> >>>> OrientedBox.cpp:(.text+0xfb): undefined reference to >>> >>>> `std::basic_ostream >& >>> >>>> std::operator<< >>> >>>> >(std::basic_ostream>> >>>> std::char_traits >&, char const*)' >>> >>>> OrientedBox.cpp:(.text+0x113): undefined reference to >>> >>>> `std::basic_ostream >& >>> >>>> std::operator<< >>> >>>>> (std::basic_ostream >&, char >>> const*)' >>> >>>> OrientedBox.cpp:(.text+0x120): undefined reference to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(double)' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In >>> >>>> function >>> >>>> `__static_initialization_and___destruction_0(int, >>> int)': >>> >>>> OrientedBox.cpp:(.text+0x3aaf)__: undefined reference >>> to >>> >>>> `std::ios_base::Init::Init()' >>> >>>> OrientedBox.cpp:(.text+0x3ab4)__: undefined reference >>> to >>> >>>> `std::ios_base::Init::~Init()' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In >>> >>>> function `moab::ErrorCode >>> >>>> moab::EigenDecomp>> moab::CartVect>(moab::Matrix3 >>> >>>> const&, double*, moab::CartVect*)': >>> >>>> >>> >>>> >>> >>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>> >>>> moab::EigenDecomp>> moab::CartVect>(moab::Matrix3 >>> >>>> const&, double*, moab::CartVect*)]+0xb7f): >>> >>>> >>> >>>> undefined >>> >>>> reference to `std::cerr' >>> >>>> >>> >>>> >>> >>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>> >>>> moab::EigenDecomp>> moab::CartVect>(moab::Matrix3 >>> >>>> const&, double*, moab::CartVect*)]+0xb84): >>> >>>> >>> >>>> undefined >>> >>>> reference to `std::basic_ostream>> std::char_traits >& >>> >>>> std::operator<< >>> >>>> >(std::basic_ostream >>> >&, char >>> >>>> const*)' >>> >>>> >>> >>>> >>> >>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>> >>>> moab::EigenDecomp>> moab::CartVect>(moab::Matrix3 >>> >>>> const&, double*, moab::CartVect*)]+0xb89): >>> >>>> >>> >>>> undefined >>> >>>> reference to `std::basic_ostream>> std::char_traits >& >>> >>>> std::endl >>> >>>> >(std::basic_ostream >>> >&)' >>> >>>> >>> >>>> >>> >>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>> >>>> moab::EigenDecomp>> moab::CartVect>(moab::Matrix3 >>> >>>> const&, double*, moab::CartVect*)]+0xb91): >>> >>>> undefined >>> >>>> reference to `std::basic_ostream>> std::char_traits >>> >>>>> ::operator<<(std::basic___ostream>> >>>> >>> >>>> std::char_traits >& (*)(std::basic_ostream>> >>>> std::char_traits >&))' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o):(.eh_frame+__0x22f): >>> >>>> undefined reference to >>> >>>> >>> >>>> `__gxx_personality_v0' >>> >>>> collect2: ld returned 1 exit status >>> >>>> make: *** [nek5000] Error 1 >>> >>>> >>> >>>> Thanks, >>> >>>> Ami >>> >>>> >>> >>>> >>> >>>> _________________________________________________ >>> >>>> Nek5000-users mailing list >>> >>>> Nek5000-users at lists.mcs.anl.__gov >>> >>>> >>> >>>> >>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >>> >>>> >>> >>> >>>> >>> >>>> >>> >>>> -- >>> >>>> >>> ==============================__==============================__==== >>> >>>> >>> >>>> "You will keep in perfect peace him whose mind is >>> >>>> steadfast, because he trusts in you." >>> Isaiah 26:3 >>> >>>> >>> >>>> Tim Tautges Argonne National >>> Laboratory >>> >>>> (tautges at mcs.anl.gov >>> ) >>> >>>> (telecommuting from UW-Madison) >>> >>>> phone (gvoice): (608) 354-1459 >>> 1500 >>> >>>> Engineering Dr. >>> >>>> fax: (608) 263-4499 >>> >>> >>>> Madison, WI 53706 >>> >>>> >>> >>>> _________________________________________________ >>> >>>> Nek5000-users mailing list >>> >>>> Nek5000-users at lists.mcs.anl.__gov >>> >>>> >>> >>>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> _______________________________________________ >>> >>>> Nek5000-users mailing list >>> >>>> Nek5000-users at lists.mcs.anl.gov >>> >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >>>> >>> >>> >>> >>> -- >>> >>> ================================================================ >>> >>> "You will keep in perfect peace him whose mind is >>> >>> steadfast, because he trusts in you." Isaiah >>> 26:3 >>> >>> >>> >>> Tim Tautges Argonne National Laboratory >>> >>> (tautges at mcs.anl.gov) (telecommuting from >>> UW-Madison) >>> >>> phone (gvoice): (608) 354-1459 1500 Engineering Dr. >>> >>> fax: (608) 263-4499 Madison, WI 53706 >>> >>> >>> >>> _______________________________________________ >>> >>> Nek5000-users mailing list >>> >>> Nek5000-users at lists.mcs.anl.gov >>> >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> >>> >> >>> >> >>> >> _______________________________________________ >>> >> Nek5000-users mailing list >>> >> Nek5000-users at lists.mcs.anl.gov >>> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> >>> > >>> >>> -- >>> ================================================================ >>> "You will keep in perfect peace him whose mind is >>> steadfast, because he trusts in you." Isaiah 26:3 >>> >>> Tim Tautges Argonne National Laboratory >>> (tautges at mcs.anl.gov) (telecommuting from UW-Madison) >>> phone (gvoice): (608) 354-1459 1500 Engineering Dr. >>> fax: (608) 263-4499 Madison, WI 53706 >>> >>> >> >> -- >> ================================================================ >> "You will keep in perfect peace him whose mind is >> steadfast, because he trusts in you." Isaiah 26:3 >> >> Tim Tautges Argonne National Laboratory >> (tautges at mcs.anl.gov) (telecommuting from UW-Madison) >> phone (gvoice): (608) 354-1459 1500 Engineering Dr. >> fax: (608) 263-4499 Madison, WI 53706 >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Sep 13 09:39:26 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 13 Sep 2013 10:39:26 -0400 Subject: [Nek5000-users] Running MOAB example In-Reply-To: References: <192817286.8839645.1378919428460.JavaMail.root@mcs.anl.gov> Message-ID: I added this hdf5 library, but thereis one not founded library (libmpi_cxx.so.1) abd when I set it with export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/openmpi/lib/, it gives me fatal error like this [amirreza at biofluids moab]$ ./nek5000 pipe Fatal error in PMPI_Comm_dup: Invalid communicator, error stack: PMPI_Comm_dup(175): MPI_Comm_dup(comm=0x0, new_comm=0x7fff496883ac) failed PMPI_Comm_dup(133): Invalid communicator what should I do now? I checked this library and I just have it in /usr/local/lib/ and /usr/lib64/openmpi/lib/ which both of them not working! Thanks, Ami On Thu, Sep 12, 2013 at 2:49 PM, wrote: > If you HDF5 and NetCDF are configured as shared libraries, make sure > their library paths are included in LD_LIBRARY_PATH. e.g., > > export > LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/amirreza/Amirreza/hdf5-1.8.11/lib > > Also check > > ldd ./nek5000 > > to make sure that all the necessary libraries are being resolved > correctly before attempting to run the code again. > > Vijay > > On Thu, Sep 12, 2013 at 1:43 PM, wrote: > > Hi All, > > > > After fixing MOAB, I successully compiled MOAB example but when I tried > > ./nek pipe, it gave me this error > > > > mv: cannot stat `pipe.log': No such file or directory > > ./nek5000: error while loading shared libraries: libhdf5.so.8: cannot > open > > shared object file: No such file or directory > > > > real 0m0.001s > > user 0m0.000s > > sys 0m0.000s > > > > can any one tell me what is the problem? FYI, I am using hdf5-1.8.11 with > > zlib-1.2.5 and szip-2.1. > > > > Thanks, > > Ami > > > > > > On Wed, Sep 11, 2013 at 1:30 PM, > wrote: > >> > >> > >> > >> On 09/11/2013 12:10 PM, Iulian Grindeanu wrote: > >>> > >>> > >>> > >>> > >>> > ------------------------------------------------------------------------------------------------------------------------ > >>> > >>> > >>> Aha, good catch. > >>> > >>> Iulian, could you backport the imesh_freememory function? Thanks. > >>> > >>> Hello, > >>> The Version 4.6 was released on February 11. The link to the tar ball > is > >>> in the web page. > >>> http://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB > >>> > >>> http://ftp.mcs.anl.gov/pub/fathom/moab-4.6.0.tar.gz > >>> (so this is the official release 4.6) > >>> > >>> The current Version4.6 branch, in the git repository, already has the > >>> free memory function backported. > >>> That tarball is updated nightly, and you can get it from this link (on > >>> the moab wiki page too) > >>> > >>> http://ftp.mcs.anl.gov/pub/fathom/moab-4.6-nightly.tar.gz > >>> > >>> Is this what they need? > >>> > >> > >> Ok, yes, that's what they need, thanks. > >> > >> - tim > >> > >> > >>> Thanks, > >>> Iulian > >>> > >>> - tim > >>> > >>> On 09/11/2013 11:33 AM, Vijay S. Mahadevan wrote: > >>> > The linker error is because of your version mismatch. You need > to > >>> > update your moab to the latest version. I see you are using v4.6 > >>> now. > >>> > You should be able to use the dev version from > >>> > https://bitbucket.org/fathomteam/moab with git or download the > >>> newer > >>> > patch from https://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB. > >>> > > >>> > Tim, can we create a new patched version of the release for > >>> download. > >>> > I spoke to Rajeev about this some time back but we need to > decide > >>> what > >>> > fixes to backport. > >>> > > >>> > Vijay > >>> > > >>> > On Wed, Sep 11, 2013 at 11:20 AM, > >>> wrote: > >>> >> > >>> >> Yes , I am using gnu, and whwen I add USR_LFLAGS="-lmpi_cxx > >>> -lstdc++, > >>> >> I get this, > >>> >> makenek - automatic build tool for Nek5000 > >>> >> generating makefile ... > >>> >> mpif77 -c -O2 -fdefault-real-8 -x f77-cpp-input -fcray-pointer > >>> -DMOAB > >>> >> -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG > >>> >> -I/home/amirreza/nek5_svn/amirreza_test/examples/moab > >>> >> -I/home/amirreza/nek5_svn/trunk/nek -I./ > >>> >> /home/amirreza/nek5_svn/amirreza_test/examples/moab/pipe.f > >>> >> -I/home/amirreza/nek5_svn/trunk/nek/3rd_party > >>> >> -I/home/amirreza/Amirreza/moab-4.6.0/gcc/include -o obj/pipe.o > >>> >> mpif77 -o nek5000 obj/pipe.o obj/drive.o obj/drive1.o > >>> obj/drive2.o > >>> >> obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o > >>> >> obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o > obj/gauss.o > >>> >> obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o > >>> obj/navier2.o > >>> >> obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o > >>> obj/map2.o > >>> >> obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o > >>> obj/math.o > >>> >> obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o > >>> >> obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o > obj/gmres.o > >>> obj/hsmg.o > >>> >> obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o > >>> obj/navier6.o > >>> >> obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o > obj/calcz.o > >>> obj/byte.o > >>> >> obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o > >>> >> obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o > >>> >> obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o > >>> obj/dsygv.o > >>> >> obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o > >>> obj/imeshutil.o > >>> >> obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o > >>> obj/jl_sort.o > >>> >> obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o > >>> >> obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o > >>> >> obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o > >>> obj/jl_obbox.o > >>> >> obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o > >>> obj/jl_findpts_el_2.o > >>> >> obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o > >>> >> -L/home/amirreza/Amirreza/netcdf-4.1.3/gcc/lib > >>> >> -L/home/amirreza/Amirreza/zlib-1.2.5/gcc/lib > >>> >> -L/home/amirreza/Amirreza/szip-2.1/gcc/lib > >>> >> -L/home/amirreza/Amirreza/hdf5-1.8.11/lib > >>> >> -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib > >>> >> -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib -liMesh -lMOAB > >>> -lnetcdf -lhdf5 > >>> >> -lsz -lm -lmpi_cxx -lstdc++ > >>> >> obj/moab.o: In function `nekmoab_intbc_': > >>> >> moab.f:(.text+0xe9d): undefined reference to > `imesh_freememory_' > >>> >> moab.f:(.text+0xece): undefined reference to > `imesh_freememory_' > >>> >> moab.f:(.text+0xee4): undefined reference to > `imesh_freememory_' > >>> >> moab.f:(.text+0xf05): undefined reference to > `imesh_freememory_' > >>> >> obj/moab.o: In function `nekmoab_bc_': > >>> >> moab.f:(.text+0x1306): undefined reference to > `imesh_freememory_' > >>> >> > >>> >> collect2: ld returned 1 exit status > >>> >> make: *** [nek5000] Error 1 > >>> >> > >>> >> Thanks, > >>> >> Ami > >>> >> > >>> >> > >>> >> On Wed, Sep 11, 2013 at 12:05 PM, > >>> wrote: > >>> >>> > >>> >>> It depends which compiler you're using. Are you using gnu? > >>> >>> > >>> >>> Please send complete compile output. > >>> >>> > >>> >>> - tim > >>> >>> > >>> >>> > >>> >>> On 09/11/2013 10:11 AM, nek5000-users at lists.mcs.anl.govwrote: > >>> >>>> > >>> >>>> Thanks for your answer, to make sure I have added libraries > to > >>> makenek > >>> >>>> ''USR_LFLAGS="-lmpi_cxx -lstdc++" which I'm > >>> >>>> getting same error,so you mean I need to add appropriate > >>> fortran library > >>> >>>> to USR_LFLAGS? > >>> >>>> > >>> >>>> Thanks, > >>> >>>> Ami > >>> >>>> > >>> >>>> > >>> >>>> On Wed, Sep 11, 2013 at 10:47 AM, > >>> >>> >>>> > wrote: > >>> >>>> > >>> >>>> Hi Ami, > >>> >>>> That's the C++ runtime. You have two options: > >>> >>>> 1. Link with the C++ compiler; in this case, you'll have > >>> to > >>> >>>> explicitly add the fortran runtime libraries to the link > >>> >>>> statement, which is most easily done by adding it to > >>> USR_LFLAGS in > >>> >>>> makenek. Compiler documents often tell you which > >>> >>>> libraries implement the fortran runtime, usually in a > >>> section about > >>> >>>> inter-language linking. > >>> >>>> > >>> >>>> 2. Add the C++ std libs to USR_LFLAGS. The > >>> trunk/nek/makenek file > >>> >>>> has a few examples of this method for > >>> >>>> gnu/intel/pgi. Sometimes, like on BG/x, it can be > >>> difficult to > >>> >>>> figure out what all comprises the C++ runtime, which > >>> >>>> is why I list 1. above. > >>> >>>> > >>> >>>> - tim > >>> >>>> > >>> >>>> > >>> >>>> On 09/11/2013 09:31 AM, nek5000-users at lists.mcs.anl. > __gov > >>> >>>> wrote: > >>> >>>> > >>> >>>> Hello Neks, > >>> >>>> > >>> >>>> I am trying to run MOAB example with nek5000, but > all > >>> the time > >>> >>>> which I am running, it gives me set of undefined > >>> >>>> reference error. I put an error with last part of my > >>> ./makenek > >>> >>>> pipe log below. > >>> >>>> What is wrong with my work? > >>> >>>> > >>> >>>> IODebugTrack.cpp:(.text+0xb74)__: undefined > reference > >>> to > >>> >>>> `std::basic_ostream >& > >>> >>>> > >>> >>>> std::operator<< > >>> >>>>> (std::basic_ostream >&, char > >>> const*)' > >>> >>>> IODebugTrack.cpp:(.text+0xb7f)__: undefined > reference > >>> to > >>> >>>> `std::basic_ostream > >>> >>>> >::operator<<(unsigned long)' > >>> >>>> IODebugTrack.cpp:(.text+0xb8c)__: undefined > reference > >>> to > >>> >>>> `std::basic_ostream >& > >>> >>>> > >>> >>>> std::operator<< > >>> >>>>> (std::basic_ostream >&, char > >>> const*)' > >>> >>>> IODebugTrack.cpp:(.text+0xb97)__: undefined > reference > >>> to > >>> >>>> `std::basic_ostream > >>> >>>> >::operator<<(unsigned long)' > >>> >>>> IODebugTrack.cpp:(.text+0xbd3)__: undefined > reference > >>> to > >>> >>>> `std::basic_ostream >& > >>> >>>> > >>> >>>> std::operator<< > >>> >>>>> (std::basic_ostream >&, char > >>> const*)' > >>> >>>> IODebugTrack.cpp:(.text+0xbde)__: undefined > reference > >>> to > >>> >>>> `std::basic_ostream > >>> >>>> >::operator<<(unsigned long)' > >>> >>>> IODebugTrack.cpp:(.text+0xbeb)__: undefined > reference > >>> to > >>> >>>> `std::basic_ostream >& > >>> >>>> > >>> >>>> std::operator<< > >>> >>>>> (std::basic_ostream >&, char > >>> const*)' > >>> >>>> IODebugTrack.cpp:(.text+0xbf6)__: undefined > reference > >>> to > >>> >>>> `std::basic_ostream > >>> >>>> >::operator<<(unsigned long)' > >>> >>>> IODebugTrack.cpp:(.text+0xc03)__: undefined > reference > >>> to > >>> >>>> `std::basic_ostream >& > >>> >>>> > >>> >>>> std::operator<< > >>> >>>>> (std::basic_ostream >&, char > >>> const*)' > >>> >>>> IODebugTrack.cpp:(.text+0xc0e)__: undefined > reference > >>> to > >>> >>>> `std::basic_ostream > >>> >>>> >::operator<<(unsigned long)' > >>> >>>> IODebugTrack.cpp:(.text+0xc1b)__: undefined > reference > >>> to > >>> >>>> `std::basic_ostream >& > >>> >>>> > >>> >>>> std::operator<< > >>> >>>>> (std::basic_ostream >&, char > >>> const*)' > >>> >>>> IODebugTrack.cpp:(.text+0xc26)__: undefined > reference > >>> to > >>> >>>> `std::basic_ostream > >>> >>>> >::operator<<(unsigned long)' > >>> >>>> IODebugTrack.cpp:(.text+0xc33)__: undefined > reference > >>> to > >>> >>>> `std::basic_ostream >& > >>> >>>> > >>> >>>> std::operator<< > >>> >>>>> (std::basic_ostream >&, char > >>> const*)' > >>> >>>> IODebugTrack.cpp:(.text+0xc38)__: undefined > reference > >>> to > >>> >>>> `std::basic_ostream >& > >>> >>>> > >>> >>>> std::endl > >>> >(std::basic_ostream >>> >>>> std::char_traits >&)' > >>> >>>> IODebugTrack.cpp:(.text+0xc40)__: undefined > reference > >>> to > >>> >>>> `std::basic_ostream > >>> >>>> >::operator<<(std::basic___ostream >>> std::char_traits > >>> >>>>> & (*)(std::basic_ostream >>> >>>> std::char_traits >&))' > >>> >>>> IODebugTrack.cpp:(.text+0xc50)__: undefined > reference > >>> to > >>> >>>> `std::basic_ostream > >>> >>>> >::flush()' > >>> >>>> > >>> >>>> > >>> > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In > >>> >>>> function > >>> >>>> `moab::IODebugTrack::all___reduce()': > >>> >>>> IODebugTrack.cpp:(.text+0xd08)__: undefined > reference > >>> to > >>> >>>> `MPI_Comm_size' > >>> >>>> IODebugTrack.cpp:(.text+0xdfe)__: undefined > reference > >>> to > >>> >>>> `MPI_Gather' > >>> >>>> IODebugTrack.cpp:(.text+__0x1080): undefined > reference > >>> to > >>> >>>> `MPI_Gatherv' > >>> >>>> > >>> >>>> > >>> > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In > >>> >>>> function > >>> >>>> `__static_initialization_and___destruction_0(int, > >>> int)': > >>> >>>> IODebugTrack.cpp:(.text+__0x1221): undefined > reference > >>> to > >>> >>>> `std::ios_base::Init::Init()' > >>> >>>> IODebugTrack.cpp:(.text+__0x1226): undefined > reference > >>> to > >>> >>>> `std::ios_base::Init::~Init()' > >>> >>>> > >>> >>>> > >>> > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In > >>> >>>> function > >>> >>>> `std::list >>> >>>> std::allocator > >>> >>>>> > >>> ::_M_insert(std::_List___iterator, > >>> >>>> moab::IODebugTrack::DRange const&)': > >>> >>>> > >>> >>>> > >>> > >>> > IODebugTrack.cpp:(.text.___ZNSt4listIN4moab12IODebugTrack__6DRangeESaIS2_EE9_M___insertESt14_List_iteratorIS2___ERKS2_[std::list >>> >>>> std::allocator > >>> >>>>> > >>> ::_M_insert(std::_List___iterator, > >>> >>>> > >>> >>>> moab::IODebugTrack::DRange const&)]+0x3a): undefined > >>> reference to > >>> >>>> > >>> >>>> > >>> > `std::__detail::_List_node___base::_M_hook(std::__detail::___List_node_base*)' > >>> >>>> > >>> >>>> > >>> > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In > >>> >>>> function > >>> >>>> > >>> >>>> > >>> > `__gnu_cxx::new_allocator > >>> >>>> > >>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, > >>> >>>> unsigned long)': > >>> >>>> > >>> >>>> > >>> > >>> > IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE10deallocateEPS5_m[__gnu___cxx::new_allocator > >>> >>>> > >>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, > >>> >>>> unsigned long)]+0x1c): undefined reference to > >>> >>>> `operator > >>> >>>> delete(void*)' > >>> >>>> > >>> >>>> > >>> > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In > >>> >>>> function > >>> >>>> > >>> >>>> > >>> > `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__allocate(unsigned > >>> >>>> long, void const*)': > >>> >>>> > >>> >>>> > >>> > >>> > IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned > >>> >>>> > >>> >>>> long, void const*)]+0x2c): undefined reference to > >>> >>>> `std::__throw_bad_alloc()' > >>> >>>> > >>> >>>> > >>> > >>> > IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned > >>> >>>> > >>> >>>> long, void const*)]+0x45): undefined reference to > >>> `operator > >>> >>>> new(unsigned long)' > >>> >>>> > >>> >>>> > >>> > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In > >>> >>>> function > >>> >>>> > >>> >>>> > >>> > `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__deallocate(moab::IODebugTrack:__:DRange*, > >>> >>>> unsigned > >>> >>>> long)': > >>> >>>> > >>> >>>> > >>> > >>> > IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE10deallocateEPS3_m[____gnu_cxx::new_allocator::__deallocate(moab::IODebugTrack:__:DRange*, > >>> >>>> > >>> >>>> unsigned long)]+0x1c): undefined reference to > >>> `operator > >>> >>>> delete(void*)' > >>> >>>> > >>> >>>> > >>> > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In > >>> >>>> function > >>> >>>> > >>> >>>> > >>> > `__gnu_cxx::new_allocator > >>> >>>>> ::allocate(unsigned long, void const*)': > >>> >>>> > >>> >>>> > >>> > >>> > IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator > >>> >>>> > >>> >>>> >::allocate(unsigned long, void const*)]+0x2c): > >>> undefined > >>> >>>> reference to `std::__throw_bad_alloc()' > >>> >>>> > >>> >>>> > >>> > >>> > IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator > >>> >>>> > >>> >>>> >::allocate(unsigned long, void const*)]+0x46): > >>> undefined > >>> >>>> reference to `operator new(unsigned long)' > >>> >>>> > >>> >>>> > >>> > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o):(.eh_frame+__0x24b): > >>> >>>> undefined reference to > >>> >>>> `__gxx_personality_v0' > >>> >>>> > >>> >>>> > >>> > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In > >>> >>>> function > >>> >>>> `moab::operator<<(std::basic___ostream >>> >>>> std::char_traits >&, moab::OrientedBox const&)': > >>> >>>> > >>> >>>> OrientedBox.cpp:(.text+0x97): undefined reference to > >>> >>>> `std::basic_ostream >& > >>> >>>> std::operator<< > >>> >>>> >(std::basic_ostream >>> >>>> std::char_traits >&, char const*)' > >>> >>>> OrientedBox.cpp:(.text+0xaf): undefined reference to > >>> >>>> `std::basic_ostream >& > >>> >>>> std::operator<< > >>> >>>> >(std::basic_ostream >>> >>>> std::char_traits >&, char const*)' > >>> >>>> OrientedBox.cpp:(.text+0xbc): undefined reference to > >>> >>>> `std::basic_ostream > >>> >>>> >::operator<<(double)' > >>> >>>> OrientedBox.cpp:(.text+0xc9): undefined reference to > >>> >>>> `std::basic_ostream >& > >>> >>>> std::operator<< > >>> >>>> >(std::basic_ostream >>> >>>> std::char_traits >&, char const*)' > >>> >>>> OrientedBox.cpp:(.text+0xe1): undefined reference to > >>> >>>> `std::basic_ostream >& > >>> >>>> std::operator<< > >>> >>>> >(std::basic_ostream >>> >>>> std::char_traits >&, char const*)' > >>> >>>> OrientedBox.cpp:(.text+0xee): undefined reference to > >>> >>>> `std::basic_ostream > >>> >>>> >::operator<<(double)' > >>> >>>> OrientedBox.cpp:(.text+0xfb): undefined reference to > >>> >>>> `std::basic_ostream >& > >>> >>>> std::operator<< > >>> >>>> >(std::basic_ostream >>> >>>> std::char_traits >&, char const*)' > >>> >>>> OrientedBox.cpp:(.text+0x113): undefined reference > to > >>> >>>> `std::basic_ostream >& > >>> >>>> std::operator<< > >>> >>>>> (std::basic_ostream >&, char > >>> const*)' > >>> >>>> OrientedBox.cpp:(.text+0x120): undefined reference > to > >>> >>>> `std::basic_ostream > >>> >>>> >::operator<<(double)' > >>> >>>> > >>> >>>> > >>> > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In > >>> >>>> function > >>> >>>> `__static_initialization_and___destruction_0(int, > >>> int)': > >>> >>>> OrientedBox.cpp:(.text+0x3aaf)__: undefined > reference > >>> to > >>> >>>> `std::ios_base::Init::Init()' > >>> >>>> OrientedBox.cpp:(.text+0x3ab4)__: undefined > reference > >>> to > >>> >>>> `std::ios_base::Init::~Init()' > >>> >>>> > >>> >>>> > >>> > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In > >>> >>>> function `moab::ErrorCode > >>> >>>> moab::EigenDecomp >>> moab::CartVect>(moab::Matrix3 > >>> >>>> const&, double*, moab::CartVect*)': > >>> >>>> > >>> >>>> > >>> > >>> > OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode > >>> >>>> moab::EigenDecomp >>> moab::CartVect>(moab::Matrix3 > >>> >>>> const&, double*, moab::CartVect*)]+0xb7f): > >>> >>>> > >>> >>>> undefined > >>> >>>> reference to `std::cerr' > >>> >>>> > >>> >>>> > >>> > >>> > OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode > >>> >>>> moab::EigenDecomp >>> moab::CartVect>(moab::Matrix3 > >>> >>>> const&, double*, moab::CartVect*)]+0xb84): > >>> >>>> > >>> >>>> undefined > >>> >>>> reference to `std::basic_ostream >>> std::char_traits >& > >>> >>>> std::operator<< > >>> >>>> >(std::basic_ostream > >>> >&, char > >>> >>>> const*)' > >>> >>>> > >>> >>>> > >>> > >>> > OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode > >>> >>>> moab::EigenDecomp >>> moab::CartVect>(moab::Matrix3 > >>> >>>> const&, double*, moab::CartVect*)]+0xb89): > >>> >>>> > >>> >>>> undefined > >>> >>>> reference to `std::basic_ostream >>> std::char_traits >& > >>> >>>> std::endl > >>> >>>> >(std::basic_ostream > >>> >&)' > >>> >>>> > >>> >>>> > >>> > >>> > OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode > >>> >>>> moab::EigenDecomp >>> moab::CartVect>(moab::Matrix3 > >>> >>>> const&, double*, moab::CartVect*)]+0xb91): > >>> >>>> undefined > >>> >>>> reference to `std::basic_ostream >>> std::char_traits > >>> >>>>> ::operator<<(std::basic___ostream >>> >>>> > >>> >>>> std::char_traits >& > (*)(std::basic_ostream >>> >>>> std::char_traits >&))' > >>> >>>> > >>> >>>> > >>> > /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o):(.eh_frame+__0x22f): > >>> >>>> undefined reference to > >>> >>>> > >>> >>>> `__gxx_personality_v0' > >>> >>>> collect2: ld returned 1 exit status > >>> >>>> make: *** [nek5000] Error 1 > >>> >>>> > >>> >>>> Thanks, > >>> >>>> Ami > >>> >>>> > >>> >>>> > >>> >>>> _________________________________________________ > >>> >>>> Nek5000-users mailing list > >>> >>>> Nek5000-users at lists.mcs.anl.__gov > >>> >>>> > >>> >>>> > >>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > >>> >>>> > >>> > >>> >>>> > >>> >>>> > >>> >>>> -- > >>> >>>> > >>> ==============================__==============================__==== > >>> >>>> > >>> >>>> "You will keep in perfect peace him whose mind is > >>> >>>> steadfast, because he trusts in you." > >>> Isaiah 26:3 > >>> >>>> > >>> >>>> Tim Tautges Argonne National > >>> Laboratory > >>> >>>> (tautges at mcs.anl.gov > >>> ) > >>> >>>> (telecommuting from UW-Madison) > >>> >>>> phone (gvoice): (608) 354-1459 > >>> 1500 > >>> >>>> Engineering Dr. > >>> >>>> fax: (608) 263-4499 > >>> > >>> >>>> Madison, WI 53706 > >>> >>>> > >>> >>>> _________________________________________________ > >>> >>>> Nek5000-users mailing list > >>> >>>> Nek5000-users at lists.mcs.anl.__gov > >>> >>>> > >>> >>>> > https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > >>> >>>> > >>> >>>> > >>> >>>> > >>> >>>> > >>> >>>> > >>> >>>> > >>> >>>> _______________________________________________ > >>> >>>> Nek5000-users mailing list > >>> >>>> Nek5000-users at lists.mcs.anl.gov > >>> >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >>> >>>> > >>> >>> > >>> >>> -- > >>> >>> > ================================================================ > >>> >>> "You will keep in perfect peace him whose mind is > >>> >>> steadfast, because he trusts in you." Isaiah > >>> 26:3 > >>> >>> > >>> >>> Tim Tautges Argonne National > Laboratory > >>> >>> (tautges at mcs.anl.gov) (telecommuting from > >>> UW-Madison) > >>> >>> phone (gvoice): (608) 354-1459 1500 Engineering Dr. > >>> >>> fax: (608) 263-4499 Madison, WI 53706 > >>> >>> > >>> >>> _______________________________________________ > >>> >>> Nek5000-users mailing list > >>> >>> Nek5000-users at lists.mcs.anl.gov > >>> >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >>> >> > >>> >> > >>> >> > >>> >> _______________________________________________ > >>> >> Nek5000-users mailing list > >>> >> Nek5000-users at lists.mcs.anl.gov > >>> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >>> >> > >>> > > >>> > >>> -- > >>> ================================================================ > >>> "You will keep in perfect peace him whose mind is > >>> steadfast, because he trusts in you." Isaiah 26:3 > >>> > >>> Tim Tautges Argonne National Laboratory > >>> (tautges at mcs.anl.gov) (telecommuting from > UW-Madison) > >>> phone (gvoice): (608) 354-1459 1500 Engineering Dr. > >>> fax: (608) 263-4499 Madison, WI 53706 > >>> > >>> > >> > >> -- > >> ================================================================ > >> "You will keep in perfect peace him whose mind is > >> steadfast, because he trusts in you." Isaiah 26:3 > >> > >> Tim Tautges Argonne National Laboratory > >> (tautges at mcs.anl.gov) (telecommuting from UW-Madison) > >> phone (gvoice): (608) 354-1459 1500 Engineering Dr. > >> fax: (608) 263-4499 Madison, WI 53706 > >> > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users at lists.mcs.anl.gov > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Sep 13 10:04:02 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 13 Sep 2013 10:04:02 -0500 Subject: [Nek5000-users] Running MOAB example In-Reply-To: References: <192817286.8839645.1378919428460.JavaMail.root@mcs.anl.gov> Message-ID: Check that you don't have multiple installations of the MPI library installed and in the path. And make sure that you consistently use only one version of MPI in all your libraries. The error might be because HDF or MOAB was not configured with your system version of OpenMPI. Check all your configuration options again. Vijay On Fri, Sep 13, 2013 at 9:39 AM, wrote: > I added this hdf5 library, but thereis one not founded library > (libmpi_cxx.so.1) abd when I set it with export > LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/openmpi/lib/, it gives me fatal > error like this > [amirreza at biofluids moab]$ ./nek5000 pipe > Fatal error in PMPI_Comm_dup: Invalid communicator, error stack: > PMPI_Comm_dup(175): MPI_Comm_dup(comm=0x0, new_comm=0x7fff496883ac) failed > PMPI_Comm_dup(133): Invalid communicator > > what should I do now? I checked this library and I just have it in > /usr/local/lib/ and /usr/lib64/openmpi/lib/ which both of them not working! > > Thanks, > Ami > > > On Thu, Sep 12, 2013 at 2:49 PM, wrote: >> >> If you HDF5 and NetCDF are configured as shared libraries, make sure >> their library paths are included in LD_LIBRARY_PATH. e.g., >> >> export >> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/amirreza/Amirreza/hdf5-1.8.11/lib >> >> Also check >> >> ldd ./nek5000 >> >> to make sure that all the necessary libraries are being resolved >> correctly before attempting to run the code again. >> >> Vijay >> >> On Thu, Sep 12, 2013 at 1:43 PM, wrote: >> > Hi All, >> > >> > After fixing MOAB, I successully compiled MOAB example but when I tried >> > ./nek pipe, it gave me this error >> > >> > mv: cannot stat `pipe.log': No such file or directory >> > ./nek5000: error while loading shared libraries: libhdf5.so.8: cannot >> > open >> > shared object file: No such file or directory >> > >> > real 0m0.001s >> > user 0m0.000s >> > sys 0m0.000s >> > >> > can any one tell me what is the problem? FYI, I am using hdf5-1.8.11 >> > with >> > zlib-1.2.5 and szip-2.1. >> > >> > Thanks, >> > Ami >> > >> > >> > On Wed, Sep 11, 2013 at 1:30 PM, >> > wrote: >> >> >> >> >> >> >> >> On 09/11/2013 12:10 PM, Iulian Grindeanu wrote: >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> ------------------------------------------------------------------------------------------------------------------------ >> >>> >> >>> >> >>> Aha, good catch. >> >>> >> >>> Iulian, could you backport the imesh_freememory function? Thanks. >> >>> >> >>> Hello, >> >>> The Version 4.6 was released on February 11. The link to the tar ball >> >>> is >> >>> in the web page. >> >>> http://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB >> >>> >> >>> http://ftp.mcs.anl.gov/pub/fathom/moab-4.6.0.tar.gz >> >>> (so this is the official release 4.6) >> >>> >> >>> The current Version4.6 branch, in the git repository, already has the >> >>> free memory function backported. >> >>> That tarball is updated nightly, and you can get it from this link (on >> >>> the moab wiki page too) >> >>> >> >>> http://ftp.mcs.anl.gov/pub/fathom/moab-4.6-nightly.tar.gz >> >>> >> >>> Is this what they need? >> >>> >> >> >> >> Ok, yes, that's what they need, thanks. >> >> >> >> - tim >> >> >> >> >> >>> Thanks, >> >>> Iulian >> >>> >> >>> - tim >> >>> >> >>> On 09/11/2013 11:33 AM, Vijay S. Mahadevan wrote: >> >>> > The linker error is because of your version mismatch. You need >> >>> to >> >>> > update your moab to the latest version. I see you are using >> >>> v4.6 >> >>> now. >> >>> > You should be able to use the dev version from >> >>> > https://bitbucket.org/fathomteam/moab with git or download the >> >>> newer >> >>> > patch from https://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB. >> >>> > >> >>> > Tim, can we create a new patched version of the release for >> >>> download. >> >>> > I spoke to Rajeev about this some time back but we need to >> >>> decide >> >>> what >> >>> > fixes to backport. >> >>> > >> >>> > Vijay >> >>> > >> >>> > On Wed, Sep 11, 2013 at 11:20 AM, >> >>> wrote: >> >>> >> >> >>> >> Yes , I am using gnu, and whwen I add USR_LFLAGS="-lmpi_cxx >> >>> -lstdc++, >> >>> >> I get this, >> >>> >> makenek - automatic build tool for Nek5000 >> >>> >> generating makefile ... >> >>> >> mpif77 -c -O2 -fdefault-real-8 -x f77-cpp-input >> >>> -fcray-pointer >> >>> -DMOAB >> >>> >> -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG >> >>> >> -I/home/amirreza/nek5_svn/amirreza_test/examples/moab >> >>> >> -I/home/amirreza/nek5_svn/trunk/nek -I./ >> >>> >> /home/amirreza/nek5_svn/amirreza_test/examples/moab/pipe.f >> >>> >> -I/home/amirreza/nek5_svn/trunk/nek/3rd_party >> >>> >> -I/home/amirreza/Amirreza/moab-4.6.0/gcc/include -o >> >>> obj/pipe.o >> >>> >> mpif77 -o nek5000 obj/pipe.o obj/drive.o obj/drive1.o >> >>> obj/drive2.o >> >>> >> obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o >> >>> >> obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o >> >>> obj/gauss.o >> >>> >> obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o >> >>> obj/navier2.o >> >>> >> obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o >> >>> obj/map2.o >> >>> >> obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o >> >>> obj/math.o >> >>> >> obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o >> >>> >> obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o >> >>> obj/gmres.o >> >>> obj/hsmg.o >> >>> >> obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o >> >>> obj/navier6.o >> >>> >> obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o >> >>> obj/calcz.o >> >>> obj/byte.o >> >>> >> obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o >> >>> >> obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o >> >>> >> obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o >> >>> obj/dsygv.o >> >>> >> obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o >> >>> obj/imeshutil.o >> >>> >> obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o >> >>> obj/jl_sort.o >> >>> >> obj/jl_sarray_transfer.o obj/jl_sarray_sort.o >> >>> obj/jl_gs_local.o >> >>> >> obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o >> >>> >> obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o >> >>> obj/jl_obbox.o >> >>> >> obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o >> >>> obj/jl_findpts_el_2.o >> >>> >> obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o >> >>> >> -L/home/amirreza/Amirreza/netcdf-4.1.3/gcc/lib >> >>> >> -L/home/amirreza/Amirreza/zlib-1.2.5/gcc/lib >> >>> >> -L/home/amirreza/Amirreza/szip-2.1/gcc/lib >> >>> >> -L/home/amirreza/Amirreza/hdf5-1.8.11/lib >> >>> >> -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib >> >>> >> -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib -liMesh -lMOAB >> >>> -lnetcdf -lhdf5 >> >>> >> -lsz -lm -lmpi_cxx -lstdc++ >> >>> >> obj/moab.o: In function `nekmoab_intbc_': >> >>> >> moab.f:(.text+0xe9d): undefined reference to >> >>> `imesh_freememory_' >> >>> >> moab.f:(.text+0xece): undefined reference to >> >>> `imesh_freememory_' >> >>> >> moab.f:(.text+0xee4): undefined reference to >> >>> `imesh_freememory_' >> >>> >> moab.f:(.text+0xf05): undefined reference to >> >>> `imesh_freememory_' >> >>> >> obj/moab.o: In function `nekmoab_bc_': >> >>> >> moab.f:(.text+0x1306): undefined reference to >> >>> `imesh_freememory_' >> >>> >> >> >>> >> collect2: ld returned 1 exit status >> >>> >> make: *** [nek5000] Error 1 >> >>> >> >> >>> >> Thanks, >> >>> >> Ami >> >>> >> >> >>> >> >> >>> >> On Wed, Sep 11, 2013 at 12:05 PM, >> >>> wrote: >> >>> >>> >> >>> >>> It depends which compiler you're using. Are you using gnu? >> >>> >>> >> >>> >>> Please send complete compile output. >> >>> >>> >> >>> >>> - tim >> >>> >>> >> >>> >>> >> >>> >>> On 09/11/2013 10:11 AM, nek5000-users at lists.mcs.anl.gov >> >>> wrote: >> >>> >>>> >> >>> >>>> Thanks for your answer, to make sure I have added libraries >> >>> to >> >>> makenek >> >>> >>>> ''USR_LFLAGS="-lmpi_cxx -lstdc++" which I'm >> >>> >>>> getting same error,so you mean I need to add appropriate >> >>> fortran library >> >>> >>>> to USR_LFLAGS? >> >>> >>>> >> >>> >>>> Thanks, >> >>> >>>> Ami >> >>> >>>> >> >>> >>>> >> >>> >>>> On Wed, Sep 11, 2013 at 10:47 AM, >> >>> > >>> >>>> > wrote: >> >>> >>>> >> >>> >>>> Hi Ami, >> >>> >>>> That's the C++ runtime. You have two options: >> >>> >>>> 1. Link with the C++ compiler; in this case, you'll >> >>> have >> >>> to >> >>> >>>> explicitly add the fortran runtime libraries to the link >> >>> >>>> statement, which is most easily done by adding it to >> >>> USR_LFLAGS in >> >>> >>>> makenek. Compiler documents often tell you which >> >>> >>>> libraries implement the fortran runtime, usually in a >> >>> section about >> >>> >>>> inter-language linking. >> >>> >>>> >> >>> >>>> 2. Add the C++ std libs to USR_LFLAGS. The >> >>> trunk/nek/makenek file >> >>> >>>> has a few examples of this method for >> >>> >>>> gnu/intel/pgi. Sometimes, like on BG/x, it can be >> >>> difficult to >> >>> >>>> figure out what all comprises the C++ runtime, which >> >>> >>>> is why I list 1. above. >> >>> >>>> >> >>> >>>> - tim >> >>> >>>> >> >>> >>>> >> >>> >>>> On 09/11/2013 09:31 AM, >> >>> nek5000-users at lists.mcs.anl.__gov >> >>> >>>> wrote: >> >>> >>>> >> >>> >>>> Hello Neks, >> >>> >>>> >> >>> >>>> I am trying to run MOAB example with nek5000, but >> >>> all >> >>> the time >> >>> >>>> which I am running, it gives me set of undefined >> >>> >>>> reference error. I put an error with last part of >> >>> my >> >>> ./makenek >> >>> >>>> pipe log below. >> >>> >>>> What is wrong with my work? >> >>> >>>> >> >>> >>>> IODebugTrack.cpp:(.text+0xb74)__: undefined >> >>> reference >> >>> to >> >>> >>>> `std::basic_ostream >& >> >>> >>>> >> >>> >>>> std::operator<< >> >>> >>>>> (std::basic_ostream >&, char >> >>> const*)' >> >>> >>>> IODebugTrack.cpp:(.text+0xb7f)__: undefined >> >>> reference >> >>> to >> >>> >>>> `std::basic_ostream >> >>> >>>> >::operator<<(unsigned long)' >> >>> >>>> IODebugTrack.cpp:(.text+0xb8c)__: undefined >> >>> reference >> >>> to >> >>> >>>> `std::basic_ostream >& >> >>> >>>> >> >>> >>>> std::operator<< >> >>> >>>>> (std::basic_ostream >&, char >> >>> const*)' >> >>> >>>> IODebugTrack.cpp:(.text+0xb97)__: undefined >> >>> reference >> >>> to >> >>> >>>> `std::basic_ostream >> >>> >>>> >::operator<<(unsigned long)' >> >>> >>>> IODebugTrack.cpp:(.text+0xbd3)__: undefined >> >>> reference >> >>> to >> >>> >>>> `std::basic_ostream >& >> >>> >>>> >> >>> >>>> std::operator<< >> >>> >>>>> (std::basic_ostream >&, char >> >>> const*)' >> >>> >>>> IODebugTrack.cpp:(.text+0xbde)__: undefined >> >>> reference >> >>> to >> >>> >>>> `std::basic_ostream >> >>> >>>> >::operator<<(unsigned long)' >> >>> >>>> IODebugTrack.cpp:(.text+0xbeb)__: undefined >> >>> reference >> >>> to >> >>> >>>> `std::basic_ostream >& >> >>> >>>> >> >>> >>>> std::operator<< >> >>> >>>>> (std::basic_ostream >&, char >> >>> const*)' >> >>> >>>> IODebugTrack.cpp:(.text+0xbf6)__: undefined >> >>> reference >> >>> to >> >>> >>>> `std::basic_ostream >> >>> >>>> >::operator<<(unsigned long)' >> >>> >>>> IODebugTrack.cpp:(.text+0xc03)__: undefined >> >>> reference >> >>> to >> >>> >>>> `std::basic_ostream >& >> >>> >>>> >> >>> >>>> std::operator<< >> >>> >>>>> (std::basic_ostream >&, char >> >>> const*)' >> >>> >>>> IODebugTrack.cpp:(.text+0xc0e)__: undefined >> >>> reference >> >>> to >> >>> >>>> `std::basic_ostream >> >>> >>>> >::operator<<(unsigned long)' >> >>> >>>> IODebugTrack.cpp:(.text+0xc1b)__: undefined >> >>> reference >> >>> to >> >>> >>>> `std::basic_ostream >& >> >>> >>>> >> >>> >>>> std::operator<< >> >>> >>>>> (std::basic_ostream >&, char >> >>> const*)' >> >>> >>>> IODebugTrack.cpp:(.text+0xc26)__: undefined >> >>> reference >> >>> to >> >>> >>>> `std::basic_ostream >> >>> >>>> >::operator<<(unsigned long)' >> >>> >>>> IODebugTrack.cpp:(.text+0xc33)__: undefined >> >>> reference >> >>> to >> >>> >>>> `std::basic_ostream >& >> >>> >>>> >> >>> >>>> std::operator<< >> >>> >>>>> (std::basic_ostream >&, char >> >>> const*)' >> >>> >>>> IODebugTrack.cpp:(.text+0xc38)__: undefined >> >>> reference >> >>> to >> >>> >>>> `std::basic_ostream >& >> >>> >>>> >> >>> >>>> std::endl >> >>> >(std::basic_ostream> >>> >>>> std::char_traits >&)' >> >>> >>>> IODebugTrack.cpp:(.text+0xc40)__: undefined >> >>> reference >> >>> to >> >>> >>>> `std::basic_ostream >> >>> >>>> >::operator<<(std::basic___ostream> >>> std::char_traits >> >>> >>>>> & (*)(std::basic_ostream> >>> >>>> std::char_traits >&))' >> >>> >>>> IODebugTrack.cpp:(.text+0xc50)__: undefined >> >>> reference >> >>> to >> >>> >>>> `std::basic_ostream >> >>> >>>> >::flush()' >> >>> >>>> >> >>> >>>> >> >>> >> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >> >>> >>>> function >> >>> >>>> `moab::IODebugTrack::all___reduce()': >> >>> >>>> IODebugTrack.cpp:(.text+0xd08)__: undefined >> >>> reference >> >>> to >> >>> >>>> `MPI_Comm_size' >> >>> >>>> IODebugTrack.cpp:(.text+0xdfe)__: undefined >> >>> reference >> >>> to >> >>> >>>> `MPI_Gather' >> >>> >>>> IODebugTrack.cpp:(.text+__0x1080): undefined >> >>> reference >> >>> to >> >>> >>>> `MPI_Gatherv' >> >>> >>>> >> >>> >>>> >> >>> >> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >> >>> >>>> function >> >>> >>>> `__static_initialization_and___destruction_0(int, >> >>> int)': >> >>> >>>> IODebugTrack.cpp:(.text+__0x1221): undefined >> >>> reference >> >>> to >> >>> >>>> `std::ios_base::Init::Init()' >> >>> >>>> IODebugTrack.cpp:(.text+__0x1226): undefined >> >>> reference >> >>> to >> >>> >>>> `std::ios_base::Init::~Init()' >> >>> >>>> >> >>> >>>> >> >>> >> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >> >>> >>>> function >> >>> >>>> `std::list> >>> >>>> std::allocator >> >>> >>>>> >> >>> ::_M_insert(std::_List___iterator, >> >>> >>>> moab::IODebugTrack::DRange const&)': >> >>> >>>> >> >>> >>>> >> >>> >> >>> >> >>> IODebugTrack.cpp:(.text.___ZNSt4listIN4moab12IODebugTrack__6DRangeESaIS2_EE9_M___insertESt14_List_iteratorIS2___ERKS2_[std::list> >>> >>>> std::allocator >> >>> >>>>> >> >>> ::_M_insert(std::_List___iterator, >> >>> >>>> >> >>> >>>> moab::IODebugTrack::DRange const&)]+0x3a): >> >>> undefined >> >>> reference to >> >>> >>>> >> >>> >>>> >> >>> >> >>> `std::__detail::_List_node___base::_M_hook(std::__detail::___List_node_base*)' >> >>> >>>> >> >>> >>>> >> >>> >> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >> >>> >>>> function >> >>> >>>> >> >>> >>>> >> >>> >> >>> `__gnu_cxx::new_allocator >> >>> >>>> >> >>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, >> >>> >>>> unsigned long)': >> >>> >>>> >> >>> >>>> >> >>> >> >>> >> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE10deallocateEPS5_m[__gnu___cxx::new_allocator >> >>> >>>> >> >>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, >> >>> >>>> unsigned long)]+0x1c): undefined reference to >> >>> >>>> `operator >> >>> >>>> delete(void*)' >> >>> >>>> >> >>> >>>> >> >>> >> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >> >>> >>>> function >> >>> >>>> >> >>> >>>> >> >>> >> >>> `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__allocate(unsigned >> >>> >>>> long, void const*)': >> >>> >>>> >> >>> >>>> >> >>> >> >>> >> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned >> >>> >>>> >> >>> >>>> long, void const*)]+0x2c): undefined reference to >> >>> >>>> `std::__throw_bad_alloc()' >> >>> >>>> >> >>> >>>> >> >>> >> >>> >> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned >> >>> >>>> >> >>> >>>> long, void const*)]+0x45): undefined reference to >> >>> `operator >> >>> >>>> new(unsigned long)' >> >>> >>>> >> >>> >>>> >> >>> >> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >> >>> >>>> function >> >>> >>>> >> >>> >>>> >> >>> >> >>> `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__deallocate(moab::IODebugTrack:__:DRange*, >> >>> >>>> unsigned >> >>> >>>> long)': >> >>> >>>> >> >>> >>>> >> >>> >> >>> >> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE10deallocateEPS3_m[____gnu_cxx::new_allocator::__deallocate(moab::IODebugTrack:__:DRange*, >> >>> >>>> >> >>> >>>> unsigned long)]+0x1c): undefined reference to >> >>> `operator >> >>> >>>> delete(void*)' >> >>> >>>> >> >>> >>>> >> >>> >> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >> >>> >>>> function >> >>> >>>> >> >>> >>>> >> >>> >> >>> `__gnu_cxx::new_allocator >> >>> >>>>> ::allocate(unsigned long, void const*)': >> >>> >>>> >> >>> >>>> >> >>> >> >>> >> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator >> >>> >>>> >> >>> >>>> >::allocate(unsigned long, void const*)]+0x2c): >> >>> undefined >> >>> >>>> reference to `std::__throw_bad_alloc()' >> >>> >>>> >> >>> >>>> >> >>> >> >>> >> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator >> >>> >>>> >> >>> >>>> >::allocate(unsigned long, void const*)]+0x46): >> >>> undefined >> >>> >>>> reference to `operator new(unsigned long)' >> >>> >>>> >> >>> >>>> >> >>> >> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o):(.eh_frame+__0x24b): >> >>> >>>> undefined reference to >> >>> >>>> `__gxx_personality_v0' >> >>> >>>> >> >>> >>>> >> >>> >> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In >> >>> >>>> function >> >>> >>>> `moab::operator<<(std::basic___ostream> >>> >>>> std::char_traits >&, moab::OrientedBox const&)': >> >>> >>>> >> >>> >>>> OrientedBox.cpp:(.text+0x97): undefined reference >> >>> to >> >>> >>>> `std::basic_ostream >& >> >>> >>>> std::operator<< >> >>> >>>> >(std::basic_ostream> >>> >>>> std::char_traits >&, char const*)' >> >>> >>>> OrientedBox.cpp:(.text+0xaf): undefined reference >> >>> to >> >>> >>>> `std::basic_ostream >& >> >>> >>>> std::operator<< >> >>> >>>> >(std::basic_ostream> >>> >>>> std::char_traits >&, char const*)' >> >>> >>>> OrientedBox.cpp:(.text+0xbc): undefined reference >> >>> to >> >>> >>>> `std::basic_ostream >> >>> >>>> >::operator<<(double)' >> >>> >>>> OrientedBox.cpp:(.text+0xc9): undefined reference >> >>> to >> >>> >>>> `std::basic_ostream >& >> >>> >>>> std::operator<< >> >>> >>>> >(std::basic_ostream> >>> >>>> std::char_traits >&, char const*)' >> >>> >>>> OrientedBox.cpp:(.text+0xe1): undefined reference >> >>> to >> >>> >>>> `std::basic_ostream >& >> >>> >>>> std::operator<< >> >>> >>>> >(std::basic_ostream> >>> >>>> std::char_traits >&, char const*)' >> >>> >>>> OrientedBox.cpp:(.text+0xee): undefined reference >> >>> to >> >>> >>>> `std::basic_ostream >> >>> >>>> >::operator<<(double)' >> >>> >>>> OrientedBox.cpp:(.text+0xfb): undefined reference >> >>> to >> >>> >>>> `std::basic_ostream >& >> >>> >>>> std::operator<< >> >>> >>>> >(std::basic_ostream> >>> >>>> std::char_traits >&, char const*)' >> >>> >>>> OrientedBox.cpp:(.text+0x113): undefined reference >> >>> to >> >>> >>>> `std::basic_ostream >& >> >>> >>>> std::operator<< >> >>> >>>>> (std::basic_ostream >&, char >> >>> const*)' >> >>> >>>> OrientedBox.cpp:(.text+0x120): undefined reference >> >>> to >> >>> >>>> `std::basic_ostream >> >>> >>>> >::operator<<(double)' >> >>> >>>> >> >>> >>>> >> >>> >> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In >> >>> >>>> function >> >>> >>>> `__static_initialization_and___destruction_0(int, >> >>> int)': >> >>> >>>> OrientedBox.cpp:(.text+0x3aaf)__: undefined >> >>> reference >> >>> to >> >>> >>>> `std::ios_base::Init::Init()' >> >>> >>>> OrientedBox.cpp:(.text+0x3ab4)__: undefined >> >>> reference >> >>> to >> >>> >>>> `std::ios_base::Init::~Init()' >> >>> >>>> >> >>> >>>> >> >>> >> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In >> >>> >>>> function `moab::ErrorCode >> >>> >>>> moab::EigenDecomp> >>> moab::CartVect>(moab::Matrix3 >> >>> >>>> const&, double*, moab::CartVect*)': >> >>> >>>> >> >>> >>>> >> >>> >> >>> >> >>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >> >>> >>>> moab::EigenDecomp> >>> moab::CartVect>(moab::Matrix3 >> >>> >>>> const&, double*, moab::CartVect*)]+0xb7f): >> >>> >>>> >> >>> >>>> undefined >> >>> >>>> reference to `std::cerr' >> >>> >>>> >> >>> >>>> >> >>> >> >>> >> >>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >> >>> >>>> moab::EigenDecomp> >>> moab::CartVect>(moab::Matrix3 >> >>> >>>> const&, double*, moab::CartVect*)]+0xb84): >> >>> >>>> >> >>> >>>> undefined >> >>> >>>> reference to `std::basic_ostream> >>> std::char_traits >& >> >>> >>>> std::operator<< >> >>> >>>> >(std::basic_ostream >> >>> >&, char >> >>> >>>> const*)' >> >>> >>>> >> >>> >>>> >> >>> >> >>> >> >>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >> >>> >>>> moab::EigenDecomp> >>> moab::CartVect>(moab::Matrix3 >> >>> >>>> const&, double*, moab::CartVect*)]+0xb89): >> >>> >>>> >> >>> >>>> undefined >> >>> >>>> reference to `std::basic_ostream> >>> std::char_traits >& >> >>> >>>> std::endl >> >>> >>>> >(std::basic_ostream >> >>> >&)' >> >>> >>>> >> >>> >>>> >> >>> >> >>> >> >>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >> >>> >>>> moab::EigenDecomp> >>> moab::CartVect>(moab::Matrix3 >> >>> >>>> const&, double*, moab::CartVect*)]+0xb91): >> >>> >>>> undefined >> >>> >>>> reference to `std::basic_ostream> >>> std::char_traits >> >>> >>>>> ::operator<<(std::basic___ostream> >>> >>>> >> >>> >>>> std::char_traits >& >> >>> (*)(std::basic_ostream> >>> >>>> std::char_traits >&))' >> >>> >>>> >> >>> >>>> >> >>> >> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o):(.eh_frame+__0x22f): >> >>> >>>> undefined reference to >> >>> >>>> >> >>> >>>> `__gxx_personality_v0' >> >>> >>>> collect2: ld returned 1 exit status >> >>> >>>> make: *** [nek5000] Error 1 >> >>> >>>> >> >>> >>>> Thanks, >> >>> >>>> Ami >> >>> >>>> >> >>> >>>> >> >>> >>>> _________________________________________________ >> >>> >>>> Nek5000-users mailing list >> >>> >>>> Nek5000-users at lists.mcs.anl.__gov >> >>> >>>> >> >>> >>>> >> >>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >> >>> >>>> >> >>> >> >>> >>>> >> >>> >>>> >> >>> >>>> -- >> >>> >>>> >> >>> ==============================__==============================__==== >> >>> >>>> >> >>> >>>> "You will keep in perfect peace him whose mind is >> >>> >>>> steadfast, because he trusts in you." >> >>> Isaiah 26:3 >> >>> >>>> >> >>> >>>> Tim Tautges Argonne National >> >>> Laboratory >> >>> >>>> (tautges at mcs.anl.gov >> >>> ) >> >>> >>>> (telecommuting from UW-Madison) >> >>> >>>> phone (gvoice): (608) 354-1459 >> >>> 1500 >> >>> >>>> Engineering Dr. >> >>> >>>> fax: (608) 263-4499 >> >>> >> >>> >>>> Madison, WI 53706 >> >>> >>>> >> >>> >>>> _________________________________________________ >> >>> >>>> Nek5000-users mailing list >> >>> >>>> Nek5000-users at lists.mcs.anl.__gov >> >>> >>>> >> >>> >>>> >> >>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >> >>> >>>> >> >>> >>>> >> >>> >>>> >> >>> >>>> >> >>> >>>> >> >>> >>>> >> >>> >>>> _______________________________________________ >> >>> >>>> Nek5000-users mailing list >> >>> >>>> Nek5000-users at lists.mcs.anl.gov >> >>> >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >>> >>>> >> >>> >>> >> >>> >>> -- >> >>> >>> >> >>> ================================================================ >> >>> >>> "You will keep in perfect peace him whose mind is >> >>> >>> steadfast, because he trusts in you." Isaiah >> >>> 26:3 >> >>> >>> >> >>> >>> Tim Tautges Argonne National >> >>> Laboratory >> >>> >>> (tautges at mcs.anl.gov) (telecommuting from >> >>> UW-Madison) >> >>> >>> phone (gvoice): (608) 354-1459 1500 Engineering Dr. >> >>> >>> fax: (608) 263-4499 Madison, WI 53706 >> >>> >>> >> >>> >>> _______________________________________________ >> >>> >>> Nek5000-users mailing list >> >>> >>> Nek5000-users at lists.mcs.anl.gov >> >>> >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >>> >> >> >>> >> >> >>> >> >> >>> >> _______________________________________________ >> >>> >> Nek5000-users mailing list >> >>> >> Nek5000-users at lists.mcs.anl.gov >> >>> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >>> >> >> >>> > >> >>> >> >>> -- >> >>> ================================================================ >> >>> "You will keep in perfect peace him whose mind is >> >>> steadfast, because he trusts in you." Isaiah >> >>> 26:3 >> >>> >> >>> Tim Tautges Argonne National Laboratory >> >>> (tautges at mcs.anl.gov) (telecommuting from >> >>> UW-Madison) >> >>> phone (gvoice): (608) 354-1459 1500 Engineering Dr. >> >>> fax: (608) 263-4499 Madison, WI 53706 >> >>> >> >>> >> >> >> >> -- >> >> ================================================================ >> >> "You will keep in perfect peace him whose mind is >> >> steadfast, because he trusts in you." Isaiah 26:3 >> >> >> >> Tim Tautges Argonne National Laboratory >> >> (tautges at mcs.anl.gov) (telecommuting from UW-Madison) >> >> phone (gvoice): (608) 354-1459 1500 Engineering Dr. >> >> fax: (608) 263-4499 Madison, WI 53706 >> >> >> >> _______________________________________________ >> >> Nek5000-users mailing list >> >> Nek5000-users at lists.mcs.anl.gov >> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > >> > >> > >> > _______________________________________________ >> > Nek5000-users mailing list >> > Nek5000-users at lists.mcs.anl.gov >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Sep 13 10:06:24 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 13 Sep 2013 10:06:24 -0500 (CDT) Subject: [Nek5000-users] Running MOAB example In-Reply-To: Message-ID: Hi Ami, It is better to run Nek with scripts http://nek5000.mcs.anl.gov/index.php/Scripts or to be specific, in your case with a appropriate parallel script like nekbmpi Also make sure that you could run other examples in parallel (or alternatively have a MOAB build for serial execution). Aleks ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Friday, September 13, 2013 9:39:26 AM Subject: Re: [Nek5000-users] Running MOAB example I added this hdf5 library, but thereis one not founded library (libmpi_cxx.so.1) abd when I set it with export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/openmpi/lib/, it gives me fatal error like this [amirreza at biofluids moab]$ ./nek5000 pipe Fatal error in PMPI_Comm_dup: Invalid communicator, error stack: PMPI_Comm_dup(175): MPI_Comm_dup(comm=0x0, new_comm=0x7fff496883ac) failed PMPI_Comm_dup(133): Invalid communicator what should I do now? I checked this library and I just have it in /usr/local/lib/ and /usr/lib64/openmpi/lib/ which both of them not working! Thanks, Ami On Thu, Sep 12, 2013 at 2:49 PM, < nek5000-users at lists.mcs.anl.gov > wrote: If you HDF5 and NetCDF are configured as shared libraries, make sure their library paths are included in LD_LIBRARY_PATH. e.g., export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/amirreza/Amirreza/hdf5-1.8.11/lib Also check ldd ./nek5000 to make sure that all the necessary libraries are being resolved correctly before attempting to run the code again. Vijay On Thu, Sep 12, 2013 at 1:43 PM, < nek5000-users at lists.mcs.anl.gov > wrote: > Hi All, > > After fixing MOAB, I successully compiled MOAB example but when I tried > ./nek pipe, it gave me this error > > mv: cannot stat `pipe.log': No such file or directory > ./nek5000: error while loading shared libraries: libhdf5.so.8: cannot open > shared object file: No such file or directory > > real 0m0.001s > user 0m0.000s > sys 0m0.000s > > can any one tell me what is the problem? FYI, I am using hdf5-1.8.11 with > zlib-1.2.5 and szip-2.1. > > Thanks, > Ami > > > On Wed, Sep 11, 2013 at 1:30 PM, < nek5000-users at lists.mcs.anl.gov > wrote: >> >> >> >> On 09/11/2013 12:10 PM, Iulian Grindeanu wrote: >>> >>> >>> >>> >>> ------------------------------------------------------------------------------------------------------------------------ >>> >>> >>> Aha, good catch. >>> >>> Iulian, could you backport the imesh_freememory function? Thanks. >>> >>> Hello, >>> The Version 4.6 was released on February 11. The link to the tar ball is >>> in the web page. >>> http://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB >>> >>> http://ftp.mcs.anl.gov/pub/fathom/moab-4.6.0.tar.gz >>> (so this is the official release 4.6) >>> >>> The current Version4.6 branch, in the git repository, already has the >>> free memory function backported. >>> That tarball is updated nightly, and you can get it from this link (on >>> the moab wiki page too) >>> >>> http://ftp.mcs.anl.gov/pub/fathom/moab-4.6-nightly.tar.gz >>> >>> Is this what they need? >>> >> >> Ok, yes, that's what they need, thanks. >> >> - tim >> >> >>> Thanks, >>> Iulian >>> >>> - tim >>> >>> On 09/11/2013 11:33 AM, Vijay S. Mahadevan wrote: >>> > The linker error is because of your version mismatch. You need to >>> > update your moab to the latest version. I see you are using v4.6 >>> now. >>> > You should be able to use the dev version from >>> > https://bitbucket.org/fathomteam/moab with git or download the >>> newer >>> > patch from https://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB . >>> > >>> > Tim, can we create a new patched version of the release for >>> download. >>> > I spoke to Rajeev about this some time back but we need to decide >>> what >>> > fixes to backport. >>> > >>> > Vijay >>> > >>> > On Wed, Sep 11, 2013 at 11:20 AM, >>> < nek5000-users at lists.mcs.anl.gov > wrote: >>> >> >>> >> Yes , I am using gnu, and whwen I add USR_LFLAGS="-lmpi_cxx >>> -lstdc++, >>> >> I get this, >>> >> makenek - automatic build tool for Nek5000 >>> >> generating makefile ... >>> >> mpif77 -c -O2 -fdefault-real-8 -x f77-cpp-input -fcray-pointer >>> -DMOAB >>> >> -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG >>> >> -I/home/amirreza/nek5_svn/amirreza_test/examples/moab >>> >> -I/home/amirreza/nek5_svn/trunk/nek -I./ >>> >> /home/amirreza/nek5_svn/amirreza_test/examples/moab/pipe.f >>> >> -I/home/amirreza/nek5_svn/trunk/nek/3rd_party >>> >> -I/home/amirreza/Amirreza/moab-4.6.0/gcc/include -o obj/pipe.o >>> >> mpif77 -o nek5000 obj/pipe.o obj/drive.o obj/drive1.o >>> obj/drive2.o >>> >> obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o >>> >> obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o >>> >> obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o >>> obj/navier2.o >>> >> obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o >>> obj/map2.o >>> >> obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o >>> obj/math.o >>> >> obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o >>> >> obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o >>> obj/hsmg.o >>> >> obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o >>> obj/navier6.o >>> >> obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o >>> obj/byte.o >>> >> obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o >>> >> obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o >>> >> obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o >>> obj/dsygv.o >>> >> obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o >>> obj/imeshutil.o >>> >> obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o >>> obj/jl_sort.o >>> >> obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o >>> >> obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o >>> >> obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o >>> obj/jl_obbox.o >>> >> obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o >>> obj/jl_findpts_el_2.o >>> >> obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o >>> >> -L/home/amirreza/Amirreza/netcdf-4.1.3/gcc/lib >>> >> -L/home/amirreza/Amirreza/zlib-1.2.5/gcc/lib >>> >> -L/home/amirreza/Amirreza/szip-2.1/gcc/lib >>> >> -L/home/amirreza/Amirreza/hdf5-1.8.11/lib >>> >> -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib >>> >> -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib -liMesh -lMOAB >>> -lnetcdf -lhdf5 >>> >> -lsz -lm -lmpi_cxx -lstdc++ >>> >> obj/moab.o: In function `nekmoab_intbc_': >>> >> moab.f:(.text+0xe9d): undefined reference to `imesh_freememory_' >>> >> moab.f:(.text+0xece): undefined reference to `imesh_freememory_' >>> >> moab.f:(.text+0xee4): undefined reference to `imesh_freememory_' >>> >> moab.f:(.text+0xf05): undefined reference to `imesh_freememory_' >>> >> obj/moab.o: In function `nekmoab_bc_': >>> >> moab.f:(.text+0x1306): undefined reference to `imesh_freememory_' >>> >> >>> >> collect2: ld returned 1 exit status >>> >> make: *** [nek5000] Error 1 >>> >> >>> >> Thanks, >>> >> Ami >>> >> >>> >> >>> >> On Wed, Sep 11, 2013 at 12:05 PM, >>> < nek5000-users at lists.mcs.anl.gov > wrote: >>> >>> >>> >>> It depends which compiler you're using. Are you using gnu? >>> >>> >>> >>> Please send complete compile output. >>> >>> >>> >>> - tim >>> >>> >>> >>> >>> >>> On 09/11/2013 10:11 AM, nek5000-users at lists.mcs.anl.gov wrote: >>> >>>> >>> >>>> Thanks for your answer, to make sure I have added libraries to >>> makenek >>> >>>> ''USR_LFLAGS="-lmpi_cxx -lstdc++" which I'm >>> >>>> getting same error,so you mean I need to add appropriate >>> fortran library >>> >>>> to USR_LFLAGS? >>> >>>> >>> >>>> Thanks, >>> >>>> Ami >>> >>>> >>> >>>> >>> >>>> On Wed, Sep 11, 2013 at 10:47 AM, >>> < nek5000-users at lists.mcs.anl.gov >>> >>>> > wrote: >>> >>>> >>> >>>> Hi Ami, >>> >>>> That's the C++ runtime. You have two options: >>> >>>> 1. Link with the C++ compiler; in this case, you'll have >>> to >>> >>>> explicitly add the fortran runtime libraries to the link >>> >>>> statement, which is most easily done by adding it to >>> USR_LFLAGS in >>> >>>> makenek. Compiler documents often tell you which >>> >>>> libraries implement the fortran runtime, usually in a >>> section about >>> >>>> inter-language linking. >>> >>>> >>> >>>> 2. Add the C++ std libs to USR_LFLAGS. The >>> trunk/nek/makenek file >>> >>>> has a few examples of this method for >>> >>>> gnu/intel/pgi. Sometimes, like on BG/x, it can be >>> difficult to >>> >>>> figure out what all comprises the C++ runtime, which >>> >>>> is why I list 1. above. >>> >>>> >>> >>>> - tim >>> >>>> >>> >>>> >>> >>>> On 09/11/2013 09:31 AM, nek5000-users at lists.mcs.anl.__gov >>> >>>> wrote: >>> >>>> >>> >>>> Hello Neks, >>> >>>> >>> >>>> I am trying to run MOAB example with nek5000, but all >>> the time >>> >>>> which I am running, it gives me set of undefined >>> >>>> reference error. I put an error with last part of my >>> ./makenek >>> >>>> pipe log below. >>> >>>> What is wrong with my work? >>> >>>> >>> >>>> IODebugTrack.cpp:(.text+0xb74)__: undefined reference >>> to >>> >>>> `std::basic_ostream >& >>> >>>> >>> >>>> std::operator<< >>> >>>>> (std::basic_ostream >&, char >>> const*)' >>> >>>> IODebugTrack.cpp:(.text+0xb7f)__: undefined reference >>> to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(unsigned long)' >>> >>>> IODebugTrack.cpp:(.text+0xb8c)__: undefined reference >>> to >>> >>>> `std::basic_ostream >& >>> >>>> >>> >>>> std::operator<< >>> >>>>> (std::basic_ostream >&, char >>> const*)' >>> >>>> IODebugTrack.cpp:(.text+0xb97)__: undefined reference >>> to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(unsigned long)' >>> >>>> IODebugTrack.cpp:(.text+0xbd3)__: undefined reference >>> to >>> >>>> `std::basic_ostream >& >>> >>>> >>> >>>> std::operator<< >>> >>>>> (std::basic_ostream >&, char >>> const*)' >>> >>>> IODebugTrack.cpp:(.text+0xbde)__: undefined reference >>> to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(unsigned long)' >>> >>>> IODebugTrack.cpp:(.text+0xbeb)__: undefined reference >>> to >>> >>>> `std::basic_ostream >& >>> >>>> >>> >>>> std::operator<< >>> >>>>> (std::basic_ostream >&, char >>> const*)' >>> >>>> IODebugTrack.cpp:(.text+0xbf6)__: undefined reference >>> to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(unsigned long)' >>> >>>> IODebugTrack.cpp:(.text+0xc03)__: undefined reference >>> to >>> >>>> `std::basic_ostream >& >>> >>>> >>> >>>> std::operator<< >>> >>>>> (std::basic_ostream >&, char >>> const*)' >>> >>>> IODebugTrack.cpp:(.text+0xc0e)__: undefined reference >>> to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(unsigned long)' >>> >>>> IODebugTrack.cpp:(.text+0xc1b)__: undefined reference >>> to >>> >>>> `std::basic_ostream >& >>> >>>> >>> >>>> std::operator<< >>> >>>>> (std::basic_ostream >&, char >>> const*)' >>> >>>> IODebugTrack.cpp:(.text+0xc26)__: undefined reference >>> to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(unsigned long)' >>> >>>> IODebugTrack.cpp:(.text+0xc33)__: undefined reference >>> to >>> >>>> `std::basic_ostream >& >>> >>>> >>> >>>> std::operator<< >>> >>>>> (std::basic_ostream >&, char >>> const*)' >>> >>>> IODebugTrack.cpp:(.text+0xc38)__: undefined reference >>> to >>> >>>> `std::basic_ostream >& >>> >>>> >>> >>>> std::endl >>> >(std::basic_ostream>> >>>> std::char_traits >&)' >>> >>>> IODebugTrack.cpp:(.text+0xc40)__: undefined reference >>> to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(std::basic___ostream>> std::char_traits >>> >>>>> & (*)(std::basic_ostream>> >>>> std::char_traits >&))' >>> >>>> IODebugTrack.cpp:(.text+0xc50)__: undefined reference >>> to >>> >>>> `std::basic_ostream >>> >>>> >::flush()' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> >>>> function >>> >>>> `moab::IODebugTrack::all___reduce()': >>> >>>> IODebugTrack.cpp:(.text+0xd08)__: undefined reference >>> to >>> >>>> `MPI_Comm_size' >>> >>>> IODebugTrack.cpp:(.text+0xdfe)__: undefined reference >>> to >>> >>>> `MPI_Gather' >>> >>>> IODebugTrack.cpp:(.text+__0x1080): undefined reference >>> to >>> >>>> `MPI_Gatherv' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> >>>> function >>> >>>> `__static_initialization_and___destruction_0(int, >>> int)': >>> >>>> IODebugTrack.cpp:(.text+__0x1221): undefined reference >>> to >>> >>>> `std::ios_base::Init::Init()' >>> >>>> IODebugTrack.cpp:(.text+__0x1226): undefined reference >>> to >>> >>>> `std::ios_base::Init::~Init()' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> >>>> function >>> >>>> `std::list>> >>>> std::allocator >>> >>>>> >>> ::_M_insert(std::_List___iterator, >>> >>>> moab::IODebugTrack::DRange const&)': >>> >>>> >>> >>>> >>> >>> IODebugTrack.cpp:(.text.___ZNSt4listIN4moab12IODebugTrack__6DRangeESaIS2_EE9_M___insertESt14_List_iteratorIS2___ERKS2_[std::list>> >>>> std::allocator >>> >>>>> >>> ::_M_insert(std::_List___iterator, >>> >>>> >>> >>>> moab::IODebugTrack::DRange const&)]+0x3a): undefined >>> reference to >>> >>>> >>> >>>> >>> `std::__detail::_List_node___base::_M_hook(std::__detail::___List_node_base*)' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> >>>> function >>> >>>> >>> >>>> >>> `__gnu_cxx::new_allocator >>> >>>> >>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, >>> >>>> unsigned long)': >>> >>>> >>> >>>> >>> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE10deallocateEPS5_m[__gnu___cxx::new_allocator >>> >>>> >>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*, >>> >>>> unsigned long)]+0x1c): undefined reference to >>> >>>> `operator >>> >>>> delete(void*)' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> >>>> function >>> >>>> >>> >>>> >>> `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__allocate(unsigned >>> >>>> long, void const*)': >>> >>>> >>> >>>> >>> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned >>> >>>> >>> >>>> long, void const*)]+0x2c): undefined reference to >>> >>>> `std::__throw_bad_alloc()' >>> >>>> >>> >>>> >>> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator::__allocate(unsigned >>> >>>> >>> >>>> long, void const*)]+0x45): undefined reference to >>> `operator >>> >>>> new(unsigned long)' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> >>>> function >>> >>>> >>> >>>> >>> `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__deallocate(moab::IODebugTrack:__:DRange*, >>> >>>> unsigned >>> >>>> long)': >>> >>>> >>> >>>> >>> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE10deallocateEPS3_m[____gnu_cxx::new_allocator::__deallocate(moab::IODebugTrack:__:DRange*, >>> >>>> >>> >>>> unsigned long)]+0x1c): undefined reference to >>> `operator >>> >>>> delete(void*)' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In >>> >>>> function >>> >>>> >>> >>>> >>> `__gnu_cxx::new_allocator >>> >>>>> ::allocate(unsigned long, void const*)': >>> >>>> >>> >>>> >>> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator >>> >>>> >>> >>>> >::allocate(unsigned long, void const*)]+0x2c): >>> undefined >>> >>>> reference to `std::__throw_bad_alloc()' >>> >>>> >>> >>>> >>> >>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator >>> >>>> >>> >>>> >::allocate(unsigned long, void const*)]+0x46): >>> undefined >>> >>>> reference to `operator new(unsigned long)' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o):(.eh_frame+__0x24b): >>> >>>> undefined reference to >>> >>>> `__gxx_personality_v0' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In >>> >>>> function >>> >>>> `moab::operator<<(std::basic___ostream>> >>>> std::char_traits >&, moab::OrientedBox const&)': >>> >>>> >>> >>>> OrientedBox.cpp:(.text+0x97): undefined reference to >>> >>>> `std::basic_ostream >& >>> >>>> std::operator<< >>> >>>> >(std::basic_ostream>> >>>> std::char_traits >&, char const*)' >>> >>>> OrientedBox.cpp:(.text+0xaf): undefined reference to >>> >>>> `std::basic_ostream >& >>> >>>> std::operator<< >>> >>>> >(std::basic_ostream>> >>>> std::char_traits >&, char const*)' >>> >>>> OrientedBox.cpp:(.text+0xbc): undefined reference to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(double)' >>> >>>> OrientedBox.cpp:(.text+0xc9): undefined reference to >>> >>>> `std::basic_ostream >& >>> >>>> std::operator<< >>> >>>> >(std::basic_ostream>> >>>> std::char_traits >&, char const*)' >>> >>>> OrientedBox.cpp:(.text+0xe1): undefined reference to >>> >>>> `std::basic_ostream >& >>> >>>> std::operator<< >>> >>>> >(std::basic_ostream>> >>>> std::char_traits >&, char const*)' >>> >>>> OrientedBox.cpp:(.text+0xee): undefined reference to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(double)' >>> >>>> OrientedBox.cpp:(.text+0xfb): undefined reference to >>> >>>> `std::basic_ostream >& >>> >>>> std::operator<< >>> >>>> >(std::basic_ostream>> >>>> std::char_traits >&, char const*)' >>> >>>> OrientedBox.cpp:(.text+0x113): undefined reference to >>> >>>> `std::basic_ostream >& >>> >>>> std::operator<< >>> >>>>> (std::basic_ostream >&, char >>> const*)' >>> >>>> OrientedBox.cpp:(.text+0x120): undefined reference to >>> >>>> `std::basic_ostream >>> >>>> >::operator<<(double)' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In >>> >>>> function >>> >>>> `__static_initialization_and___destruction_0(int, >>> int)': >>> >>>> OrientedBox.cpp:(.text+0x3aaf)__: undefined reference >>> to >>> >>>> `std::ios_base::Init::Init()' >>> >>>> OrientedBox.cpp:(.text+0x3ab4)__: undefined reference >>> to >>> >>>> `std::ios_base::Init::~Init()' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In >>> >>>> function `moab::ErrorCode >>> >>>> moab::EigenDecomp>> moab::CartVect>(moab::Matrix3 >>> >>>> const&, double*, moab::CartVect*)': >>> >>>> >>> >>>> >>> >>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>> >>>> moab::EigenDecomp>> moab::CartVect>(moab::Matrix3 >>> >>>> const&, double*, moab::CartVect*)]+0xb7f): >>> >>>> >>> >>>> undefined >>> >>>> reference to `std::cerr' >>> >>>> >>> >>>> >>> >>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>> >>>> moab::EigenDecomp>> moab::CartVect>(moab::Matrix3 >>> >>>> const&, double*, moab::CartVect*)]+0xb84): >>> >>>> >>> >>>> undefined >>> >>>> reference to `std::basic_ostream>> std::char_traits >& >>> >>>> std::operator<< >>> >>>> >(std::basic_ostream >>> >&, char >>> >>>> const*)' >>> >>>> >>> >>>> >>> >>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>> >>>> moab::EigenDecomp>> moab::CartVect>(moab::Matrix3 >>> >>>> const&, double*, moab::CartVect*)]+0xb89): >>> >>>> >>> >>>> undefined >>> >>>> reference to `std::basic_ostream>> std::char_traits >& >>> >>>> std::endl >>> >>>> >(std::basic_ostream >>> >&)' >>> >>>> >>> >>>> >>> >>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode >>> >>>> moab::EigenDecomp>> moab::CartVect>(moab::Matrix3 >>> >>>> const&, double*, moab::CartVect*)]+0xb91): >>> >>>> undefined >>> >>>> reference to `std::basic_ostream>> std::char_traits >>> >>>>> ::operator<<(std::basic___ostream>> >>>> >>> >>>> std::char_traits >& (*)(std::basic_ostream>> >>>> std::char_traits >&))' >>> >>>> >>> >>>> >>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o):(.eh_frame+__0x22f): >>> >>>> undefined reference to >>> >>>> >>> >>>> `__gxx_personality_v0' >>> >>>> collect2: ld returned 1 exit status >>> >>>> make: *** [nek5000] Error 1 >>> >>>> >>> >>>> Thanks, >>> >>>> Ami >>> >>>> >>> >>>> >>> >>>> _________________________________________________ >>> >>>> Nek5000-users mailing list >>> >>>> Nek5000-users at lists.mcs.anl.__gov >>> >>>> >>> >>>> >>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >>> >>>> >>> < https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >>> >>>> >>> >>>> >>> >>>> -- >>> >>>> >>> ==============================__==============================__==== >>> >>>> >>> >>>> "You will keep in perfect peace him whose mind is >>> >>>> steadfast, because he trusts in you." >>> Isaiah 26:3 >>> >>>> >>> >>>> Tim Tautges Argonne National >>> Laboratory >>> >>>> ( tautges at mcs.anl.gov >>> ) >>> >>>> (telecommuting from UW-Madison) >>> >>>> phone (gvoice): (608) 354-1459 >>> 1500 >>> >>>> Engineering Dr. >>> >>>> fax: (608) 263-4499 >>> >>> >>>> Madison, WI 53706 >>> >>>> >>> >>>> _________________________________________________ >>> >>>> Nek5000-users mailing list >>> >>>> Nek5000-users at lists.mcs.anl.__gov >>> >>>> >>> >>>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >>> >>>> < https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> _______________________________________________ >>> >>>> Nek5000-users mailing list >>> >>>> Nek5000-users at lists.mcs.anl.gov >>> >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >>>> >>> >>> >>> >>> -- >>> >>> ================================================================ >>> >>> "You will keep in perfect peace him whose mind is >>> >>> steadfast, because he trusts in you." Isaiah >>> 26:3 >>> >>> >>> >>> Tim Tautges Argonne National Laboratory >>> >>> ( tautges at mcs.anl.gov ) (telecommuting from >>> UW-Madison) >>> >>> phone (gvoice): (608) 354-1459 1500 Engineering Dr. >>> >>> fax: (608) 263-4499 Madison, WI 53706 >>> >>> >>> >>> _______________________________________________ >>> >>> Nek5000-users mailing list >>> >>> Nek5000-users at lists.mcs.anl.gov >>> >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> >>> >> >>> >> >>> >> _______________________________________________ >>> >> Nek5000-users mailing list >>> >> Nek5000-users at lists.mcs.anl.gov >>> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> >>> > >>> >>> -- >>> ================================================================ >>> "You will keep in perfect peace him whose mind is >>> steadfast, because he trusts in you." Isaiah 26:3 >>> >>> Tim Tautges Argonne National Laboratory >>> ( tautges at mcs.anl.gov ) (telecommuting from UW-Madison) >>> phone (gvoice): (608) 354-1459 1500 Engineering Dr. >>> fax: (608) 263-4499 Madison, WI 53706 >>> >>> >> >> -- >> ================================================================ >> "You will keep in perfect peace him whose mind is >> steadfast, because he trusts in you." Isaiah 26:3 >> >> Tim Tautges Argonne National Laboratory >> ( tautges at mcs.anl.gov ) (telecommuting from UW-Madison) >> phone (gvoice): (608) 354-1459 1500 Engineering Dr. >> fax: (608) 263-4499 Madison, WI 53706 >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Tue Sep 24 03:38:13 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 24 Sep 2013 10:38:13 +0200 Subject: [Nek5000-users] ParaView with Nek5000 Message-ID: Dear Nek users, I'm trying to use ParaView 3.98 in order to visualize the results of a Nek5000 simulation. Starting from the output files .fld, I first create the metatada file .nek5000 (the same which can be used with VisIt). When I open this file in Paraview 3.98 all the .fld files are loaded, but the problem is that I can see only the first of these files, while the others are not visualized. Can anyone explain me the procedure to solve this problem? Thanks a lot. Matteo -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Sep 24 06:49:44 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 24 Sep 2013 06:49:44 -0500 (CDT) Subject: [Nek5000-users] ParaView with Nek5000 In-Reply-To: Message-ID: Matteo, Just guessing, but perhaps paraview is looking for geometry in the subsequent .fld files, even though it's present only in the 01 file. One test would be to create a dummy file pair, blah.fld01 blah.fld02, what are copies of the current .fld01 file and then see if paraview views both of these files. Note that if you're running on more than 1000 cores you'll likely want to switch to the .f00001 file format generated vi the IFMPIIO flag in makenek. Hope this helps, Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Tuesday, September 24, 2013 3:38:13 AM Subject: [Nek5000-users] ParaView with Nek5000 Dear Nek users, I'm trying to use ParaView 3.98 in order to visualize the results of a Nek5000 simulation. Starting from the output files .fld, I first create the metatada file .nek5000 (the same which can be used with VisIt). When I open this file in Paraview 3.98 all the .fld files are loaded, but the problem is that I can see only the first of these files, while the others are not visualized. Can anyone explain me the procedure to solve this problem? Thanks a lot. Matteo _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Wed Sep 25 04:30:31 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 25 Sep 2013 11:30:31 +0200 Subject: [Nek5000-users] ParaView with Nek5000 In-Reply-To: References: Message-ID: Hi Paul, I have tried to create a dummy file pair but it doesn't work. ParaView still views only the first file while the second file is only loaded but it isn't visualised. Matteo 2013/9/24 > > Matteo, > > Just guessing, but perhaps paraview is looking for geometry > in the subsequent .fld files, even though it's present only > in the 01 file. > > One test would be to create a dummy file pair, blah.fld01 > blah.fld02, what are copies of the current .fld01 file and then > see if paraview views both of these files. > > Note that if you're running on more than 1000 cores you'll > likely want to switch to the .f00001 file format generated > vi the IFMPIIO flag in makenek. > > Hope this helps, > > Paul > > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Sent: Tuesday, September 24, 2013 3:38:13 AM > Subject: [Nek5000-users] ParaView with Nek5000 > > > > > > > > > > Dear Nek users, > I'm trying to use ParaView 3.98 in order to visualize the results of a > Nek5000 simulation. > Starting from the output files .fld, I first create the metatada file > .nek5000 (the same which can be used with VisIt). > When I open this file in Paraview 3.98 all the .fld files are loaded, but > the problem is that I can see only the first of these files, while the > others are not visualized. > Can anyone explain me the procedure to solve this problem? > Thanks a lot. > > Matteo > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Sep 25 06:46:58 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 25 Sep 2013 06:46:58 -0500 (CDT) Subject: [Nek5000-users] ParaView with Nek5000 In-Reply-To: Message-ID: Why not use VisIt ? ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Wednesday, September 25, 2013 4:30:31 AM Subject: Re: [Nek5000-users] ParaView with Nek5000 Hi Paul, I have tried to create a dummy file pair but it doesn't work. ParaView still views only the first file while the second file is only loaded but it isn't visualised. Matteo 2013/9/24 < nek5000-users at lists.mcs.anl.gov > Matteo, Just guessing, but perhaps paraview is looking for geometry in the subsequent .fld files, even though it's present only in the 01 file. One test would be to create a dummy file pair, blah.fld01 blah.fld02, what are copies of the current .fld01 file and then see if paraview views both of these files. Note that if you're running on more than 1000 cores you'll likely want to switch to the .f00001 file format generated vi the IFMPIIO flag in makenek. Hope this helps, Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Tuesday, September 24, 2013 3:38:13 AM Subject: [Nek5000-users] ParaView with Nek5000 Dear Nek users, I'm trying to use ParaView 3.98 in order to visualize the results of a Nek5000 simulation. Starting from the output files .fld, I first create the metatada file .nek5000 (the same which can be used with VisIt). When I open this file in Paraview 3.98 all the .fld files are loaded, but the problem is that I can see only the first of these files, while the others are not visualized. Can anyone explain me the procedure to solve this problem? Thanks a lot. Matteo _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users