From nek5000-users at lists.mcs.anl.gov Thu May 2 11:13:05 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 2 May 2013 11:13:05 -0500 (CDT) Subject: [Nek5000-users] survey of apps In-Reply-To: References: Message-ID: Dear Neks, As part of a strategic planning exercise, I'd like to get a survey of performance profiles over a broad range of applications. I'm particularly interested in production runs involving lots of compute cycles, since these would be the most important for future optimization (i.e., cases where you are running 100s of simulations of more or less the same type). I'm wonder if I could ask each of you to send one or at most two logfiles directly to me - fischer at mcs.anl.gov with a very brief description giving a ballpark estimate of utilization, i.e., something like: We have run 100 of these cases, typically 6 hours each, or whatever suits. I don't really need to know anything about the app. The one thing I do need, however, is that your logfile contain the statistics that are printed at the end when the job terminates with nek's standard termination criterion (i.e., it does not stop because your run time expired). When you grep time logfile you should see something like: 163.0805685520172 7.9530425400815632E-002 eslv time 121259 153.8100430965424 7.5009415695555526E-002 pres time 121259 433.6815834045410 0.2114959564030525 crsl time 122729 0.7530927658081055 3.6726501852911642E-004 hmhz time 363777 469.4056932926178 0.2289177355990086 spro time 121260 14.56137013435364 7.1012259246232062E-003 usbc time 606294 54.14203882217407 2.6403755014022586E-002 axhm time 2070607 497.7768969535828 0.2427536813301520 advc time 363777 252.1085748672485 0.1229472179574250 vdss time 486498 7.609275102615356 3.7108583277339125E-003 dsum time 2438769 18.98749208450317 9.2597379085877490E-003 dadd time 0 1.966142654418945 9.5883993472067994E-004 ddsl time 122729 49.81083679199219 2.4291533165547920E-002 solv time 122729 22.48464226722717 1.0965212964212575E-002 prep time 121259 10.51901149749756 5.1298659712803868E-003 total elapsed time : 2.05059E+03 sec total solver time incl. I/O : 2.05054E+03 sec time/timestep : 1.69104E-02 sec CPU seconds/timestep/gridpt : 4.23184E-06 sec Preferably, the case in question should be 3D and have run for at least 100 timesteps (the more the better), so that the statistics have more significance. My plan is to build a histogram with pts/core on the x-axis, time spent where on the y axis, etc. --- something like this... By gathering this on a variety of platforms we'll be able to make more informed decisions. Thank you all! Paul From nek5000-users at lists.mcs.anl.gov Tue May 14 04:20:50 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 14 May 2013 11:20:50 +0200 Subject: [Nek5000-users] Maintaining order of perturbation Message-ID: Hi all, I want to add perturbation of specific order (e.g. 10^-08) to the whole velocity field at each time-step. The velocity and pressure are both considered on GLL points. After adding perturbation, to have velocity as continuous function across the elements dsavg() is called (I found the info in one of the threads). I think it changes the order of perturbation near to the element boundary. I was wondering if there is other way to do so. This is my first mail to the group and I am using the code for my thesis. Thanks in advance! Best regards, Sayed MSc. COSSE KTH, Sweden FAU-Erlangen,Germany From nek5000-users at lists.mcs.anl.gov Tue May 14 16:41:56 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 14 May 2013 16:41:56 -0500 (CDT) Subject: [Nek5000-users] Maintaining order of perturbation In-Reply-To: References: Message-ID: Hi Sayed, When you say it changed the order, how do you mean? It should indeed just averaged the interface values, so it should be of the same order as the initial perturbation. Paul On Tue, 14 May 2013, nek5000-users at lists.mcs.anl.gov wrote: > Hi all, > > I want to add perturbation of specific order (e.g. 10^-08) to the whole > velocity field at each time-step. The velocity and pressure are both > considered on GLL points. After adding perturbation, to have velocity as > continuous function across the elements dsavg() is called (I found the > info in one of the threads). I think it changes the order of perturbation > near to the element boundary. I was wondering if there is other way to do > so. > > This is my first mail to the group and I am using the code for my thesis. > > Thanks in advance! > > Best regards, > Sayed > MSc. COSSE > KTH, Sweden > FAU-Erlangen,Germany > > > > _______________________________________________ > 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 May 15 18:17:27 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 16 May 2013 01:17:27 +0200 Subject: [Nek5000-users] Maintaining order of perturbation In-Reply-To: References: Message-ID: Hi Paul, Sorry, I should have written it in more details. I have the base flow u_{base} calculated, already continuous across the elements. Now, I am trying to add perturbation doing to the base flow: u = u_{base}+\epsilon*u_{perturb} at each time-step. \epsilon being the order (e,g 10^-08) and u_{perturb} varies from 0 to 1 on each grid points. Best Sayed > > Hi Sayed, > > When you say it changed the order, how do you mean? > > It should indeed just averaged the interface values, so it > should be of the same order as the initial perturbation. > > Paul > > > On Tue, 14 May 2013, nek5000-users at lists.mcs.anl.gov wrote: > >> Hi all, >> >> I want to add perturbation of specific order (e.g. 10^-08) to the whole >> velocity field at each time-step. The velocity and pressure are both >> considered on GLL points. After adding perturbation, to have velocity as >> continuous function across the elements dsavg() is called (I found the >> info in one of the threads). I think it changes the order of >> perturbation >> near to the element boundary. I was wondering if there is other way to >> do >> so. >> >> This is my first mail to the group and I am using the code for my >> thesis. >> >> Thanks in advance! >> >> Best regards, >> Sayed >> MSc. COSSE >> KTH, Sweden >> FAU-Erlangen,Germany >> >> >> >> _______________________________________________ >> 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 May 15 18:29:10 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 16 May 2013 01:29:10 +0200 Subject: [Nek5000-users] Maintaining order of perturbation In-Reply-To: References: Message-ID: To add more, I found that near to the element boundary if I do the averaging(dsavg()) the order cannot be maintained at those grid points. Sayed > Hi Paul, > > Sorry, I should have written it in more details. > > I have the base flow u_{base} calculated, already continuous across the > elements. Now, I am trying to add perturbation doing to the base flow: u = > u_{base}+\epsilon*u_{perturb} at each time-step. \epsilon being the order > (e,g 10^-08) and u_{perturb} varies from 0 to 1 on each grid points. > > > Best > Sayed > >> >> Hi Sayed, >> >> When you say it changed the order, how do you mean? >> >> It should indeed just averaged the interface values, so it >> should be of the same order as the initial perturbation. >> >> Paul >> >> >> On Tue, 14 May 2013, nek5000-users at lists.mcs.anl.gov wrote: >> >>> Hi all, >>> >>> I want to add perturbation of specific order (e.g. 10^-08) to the whole >>> velocity field at each time-step. The velocity and pressure are both >>> considered on GLL points. After adding perturbation, to have velocity >>> as >>> continuous function across the elements dsavg() is called (I found the >>> info in one of the threads). I think it changes the order of >>> perturbation >>> near to the element boundary. I was wondering if there is other way to >>> do >>> so. >>> >>> This is my first mail to the group and I am using the code for my >>> thesis. >>> >>> Thanks in advance! >>> >>> Best regards, >>> Sayed >>> MSc. COSSE >>> KTH, Sweden >>> FAU-Erlangen,Germany >>> >>> >>> >>> _______________________________________________ >>> 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 May 16 07:07:20 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 16 May 2013 07:07:20 -0500 (CDT) Subject: [Nek5000-users] Maintaining order of perturbation In-Reply-To: Message-ID: Hi Sayed, Can you send me the .usr file, off-line? Best, Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Wednesday, May 15, 2013 6:29:10 PM Subject: Re: [Nek5000-users] Maintaining order of perturbation To add more, I found that near to the element boundary if I do the averaging(dsavg()) the order cannot be maintained at those grid points. Sayed > Hi Paul, > > Sorry, I should have written it in more details. > > I have the base flow u_{base} calculated, already continuous across the > elements. Now, I am trying to add perturbation doing to the base flow: u = > u_{base}+\epsilon*u_{perturb} at each time-step. \epsilon being the order > (e,g 10^-08) and u_{perturb} varies from 0 to 1 on each grid points. > > > Best > Sayed > >> >> Hi Sayed, >> >> When you say it changed the order, how do you mean? >> >> It should indeed just averaged the interface values, so it >> should be of the same order as the initial perturbation. >> >> Paul >> >> >> On Tue, 14 May 2013, nek5000-users at lists.mcs.anl.gov wrote: >> >>> Hi all, >>> >>> I want to add perturbation of specific order (e.g. 10^-08) to the whole >>> velocity field at each time-step. The velocity and pressure are both >>> considered on GLL points. After adding perturbation, to have velocity >>> as >>> continuous function across the elements dsavg() is called (I found the >>> info in one of the threads). I think it changes the order of >>> perturbation >>> near to the element boundary. I was wondering if there is other way to >>> do >>> so. >>> >>> This is my first mail to the group and I am using the code for my >>> thesis. >>> >>> Thanks in advance! >>> >>> Best regards, >>> Sayed >>> MSc. COSSE >>> KTH, Sweden >>> FAU-Erlangen,Germany >>> >>> >>> >>> _______________________________________________ >>> 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 Thu May 16 12:37:04 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 16 May 2013 19:37:04 +0200 Subject: [Nek5000-users] Axisymmetric perturbation mode Message-ID: Hi Neks! I have a very simple question, and thought I might as well ask (rather than scrutinizing the source): Does the current release of Nek5000 have an implemented (a) axisymmetric perturbation mode (b) axisymmetric perturbation mode including temperature perturbation? This means, if I set IFAXIS and IFHEAT to be true, and NPERT=-1.0, will I get the correct solution? Best regards, Outi From nek5000-users at lists.mcs.anl.gov Sun May 19 02:51:54 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 19 May 2013 10:51:54 +0300 Subject: [Nek5000-users] troubles with examples In-Reply-To: References: Message-ID: Hello everybody, I am a new nek5000 user. I have just successfully compiled the package (on my 64 bit ubuntu) and run the examples: turbChannel, vortex, turbJet. Now, although the executable seems to solve the problems (the display outputs look reasonable), the output files with *.fldxxxx etc contain only zeros (I can see that using postnek). Moreover, at the end of the run (vortex), at the summary, the output that appears on the display is as in the attachment (only zeros). Many thanks in advance, Barak Galanti -------------- next part -------------- 40021 U-PRES gmres: 1 5.8090E-16 1.0000E-07 7.9965E-16 0.0000E+00 0.0000E+00 40021 DNORM, DIVEX 9.6826759533351624E-015 5.8090008701096374E-016 40021 2.0010E+03 0.0000E+00 Fluid done 40021 2.001050E+03 -7.958699E-03 VMIN call outfld: ifpsco: F 40021 2.0010E+03 Write checkpoint: 40021 2.0010E+03 OPEN: r1854a.fld202 end of time-step loop runtime statistics: total time 9.9999999999999995E-008 inv3 time 161934 0.0000000000000000 0.0000000000000000 invc time 0 0.0000000000000000 0.0000000000000000 mltd time 605865 0.0000000000000000 0.0000000000000000 cdtp time 605865 0.0000000000000000 0.0000000000000000 eslv time 40021 0.0000000000000000 0.0000000000000000 pres time 40021 0.0000000000000000 0.0000000000000000 crsl time 41880 0.0000000000000000 0.0000000000000000 crsl min 0.0000000000000000 crsl max 0.0000000000000000 crsl avg 0.0000000000000000 hmhz time 6 0.0000000000000000 0.0000000000000000 spro time 40022 0.0000000000000000 0.0000000000000000 usbc time 40021 0.0000000000000000 0.0000000000000000 usbc min 0.0000000000000000 usbc max 0.0000000000000000 usb avg 0.0000000000000000 axhm time 888174 0.0000000000000000 0.0000000000000000 advc time 40021 0.0000000000000000 0.0000000000000000 vdss time 161935 0.0000000000000000 0.0000000000000000 vdss min 0.0000000000000000 vdss max 0.0000000000000000 vdss avg 0.0000000000000000 dsum time 893746 0.0000000000000000 0.0000000000000000 dsum min 0.0000000000000000 dsum max 0.0000000000000000 dsum avg 0.0000000000000000 dadd time 0 0.0000000000000000 0.0000000000000000 ddsl time 41880 0.0000000000000000 0.0000000000000000 solv time 41880 0.0000000000000000 0.0000000000000000 prep time 40022 0.0000000000000000 0.0000000000000000 # nid tusbc tdadd tcrsl tvdss tdsum tgop qqq F 0 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 qqq 1 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 qqq 2 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 qqq 3 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 qqq call exitt: dying ... backtrace(): obtained 5 stack frames. ./nek5000(print_stack_+0x18) [0x50e8f8] ./nek5000(exitt_+0x1d0) [0x5fa6a0] ./nek5000(main+0x3b) [0x41ae8b] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7fe09c09376d] ./nek5000() [0x41aebd] total elapsed time : 0.00000E+00 sec total solver time incl. I/O : 0.00000E+00 sec time/timestep : 0.00000E+00 sec CPU seconds/timestep/gridpt : 0.00000E+00 sec From nek5000-users at lists.mcs.anl.gov Thu May 23 10:53:34 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 23 May 2013 17:53:34 +0200 Subject: [Nek5000-users] Prenek and Genbox - Maketools problems Message-ID: Dear All, I have successfully used nek5000 with simple geometries made up of boxes and with geometries edited through the userdat2 subroutine. If I understood well, 'Prex' can be used to edit the mesh and create curved geometries/meshes right? When I try to use 'Prex' or 'Pretex' they do not work properly. The interface seems to have something wrong with it, I cannot use the program and I get errors such as: " -*-*-Medium-R-Normal--*-*-*-*-*-*-*-* I/O Error: No String Terminator sent to PRS NEKTON Version 2.6 (6144,6144,6144) (61440,61440,61440) (61440, 0, 0) (61440,61440, 0) (30720,30720,30720) ( 0, 0,61440) (61440, 0,43008) (61440,61440, 0) (43008,61440, 0) (12288,61440,12288) ( 0,61440,61440) ( 0,18432,61440) (61440, 0,61440) (61440, 0,12288) (36864,36864,36864) (30720,30720,43008) Choose a Name for This Session: XIO: fatal IO error 11 (Resource temporarily unavailable) on X server ":0" after 153 requests (153 known processed) with 0 events remaining. " I suspect it has something to do with the compilation since (even though the compilations is successful when I run 'maketools' I get the following messages for each of the tools: " ---------------------- Make prenek... ---------------------- /bin/sh: 9: [: prenek: unexpected operator /bin/sh: 12: [: prenek: unexpected operator " Another problem is that Genbox works when outputting to a .rea file but does not output a .re2 file succesfully giving the following error: " Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for this error: #0 0x7F4957D560F7 #1 0x7F4957D566D4 #2 0x7F49576B849F #3 0x412A49 in MAIN__ at genbox.f:? Segmentation fault (core dumped) " I have tried compiling with both gfortran/gcc and also with intel compilers ifort/icc but the same errors occur. Thank you in advance, JP Mollicone -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 23 10:58:48 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 23 May 2013 10:58:48 -0500 (CDT) Subject: [Nek5000-users] Prenek and Genbox - Maketools problems In-Reply-To: References: Message-ID: Dear JP, What kind of platform are you running on ? I'm certain we can straighten this out. Hopefully we can do so within the standard repo release so that it will be settled henceforth, but for certain we can resolve your specific compilation issues. We're looking into it now. Best, Paul On Thu, 23 May 2013, nek5000-users at lists.mcs.anl.gov wrote: > Dear All, > > I have successfully used nek5000 with simple geometries made up of boxes > and with geometries edited through the userdat2 subroutine. > > If I understood well, 'Prex' can be used to edit the mesh and create curved > geometries/meshes right? When I try to use 'Prex' or 'Pretex' they do not > work properly. The interface seems to have something wrong with it, I > cannot use the program and I get errors such as: > > " > -*-*-Medium-R-Normal--*-*-*-*-*-*-*-* > I/O Error: No String Terminator sent to PRS > NEKTON Version 2.6 > > (6144,6144,6144) > (61440,61440,61440) > (61440, 0, 0) > (61440,61440, 0) > (30720,30720,30720) > ( 0, 0,61440) > (61440, 0,43008) > (61440,61440, 0) > (43008,61440, 0) > (12288,61440,12288) > ( 0,61440,61440) > ( 0,18432,61440) > (61440, 0,61440) > (61440, 0,12288) > (36864,36864,36864) > (30720,30720,43008) > Choose a Name for This Session: > XIO: fatal IO error 11 (Resource temporarily unavailable) on X server ":0" > after 153 requests (153 known processed) with 0 events remaining. > " > > I suspect it has something to do with the compilation since (even though > the compilations is successful when I run 'maketools' I get the following > messages for each of the tools: > > " > ---------------------- > Make prenek... > ---------------------- > /bin/sh: 9: [: prenek: unexpected operator > /bin/sh: 12: [: prenek: unexpected operator > " > > Another problem is that Genbox works when outputting to a .rea file but > does not output a .re2 file succesfully giving the following error: > > " > Program received signal SIGSEGV: Segmentation fault - invalid memory > reference. > > Backtrace for this error: > #0 0x7F4957D560F7 > #1 0x7F4957D566D4 > #2 0x7F49576B849F > #3 0x412A49 in MAIN__ at genbox.f:? > Segmentation fault (core dumped) > " > > I have tried compiling with both gfortran/gcc and also with intel compilers > ifort/icc but the same errors occur. > > Thank you in advance, > JP Mollicone > From nek5000-users at lists.mcs.anl.gov Thu May 23 12:16:40 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 23 May 2013 19:16:40 +0200 Subject: [Nek5000-users] Prenek and Genbox - Maketools problems Message-ID: Hi Paul, Thank you for your quick reply. I am using Ubuntu 12.10 64-bit but through VMware Player running in Windows on my laptop. But I encountered the same problems on a desktop computer with Ubuntu installed on it. Thanks, JP -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 23 15:52:53 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 23 May 2013 15:52:53 -0500 Subject: [Nek5000-users] Prenek and Genbox - Maketools problems In-Reply-To: References: Message-ID: Hi JP, I think you default shell might not be pointing to bash. When you type: ls -al /bin/sh is /bin/sh pointing to bash or dash? For now, you can just change the 1st line in makefile found in nek5_svn/trunk/tools/ from: SHELL = /bin/sh to SHELL = /bin/bash I think that should correct the problems you are seeing. In the next update, I will change the script to specify bash. Best, Katie On Thu, May 23, 2013 at 12:16 PM, wrote: > Hi Paul, > > Thank you for your quick reply. > > I am using Ubuntu 12.10 64-bit but through VMware Player running in > Windows on my laptop. But I encountered the same problems on a desktop > computer with Ubuntu installed on it. > > Thanks, > JP > > _______________________________________________ > 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 May 23 16:35:28 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 23 May 2013 23:35:28 +0200 Subject: [Nek5000-users] Prenek and Genbox - Maketools problems Message-ID: Hi Katie, Yes thanks, the problem when compiling is solved. I imagined it was something related to bash but it didn't cross my mind to check the makefile. Unfortunately the errors with genbox (when trying to output a .re2 file) and prex (the errors I mentioned + interface does not work well) still remain (even after re-making the tools). Thanks, JP -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri May 24 13:10:46 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 24 May 2013 12:10:46 -0600 Subject: [Nek5000-users] Problem reading restart data Message-ID: Hello Neks. We just got a new system and I'm trying to run some nek cases that worked fine on our previous systems. Everything seems fine when running without having to read initial condition data. However, I'm having a problem reading in restart data, e.g., from the log file: " Error reading initial condition/drive force data aborting in routine rdicdf. EXIT: rdicdf error 1 call exitt: dying ? " Our new system has the Xeon E5-2670 "SandyBridge" cores and FDR (Fourteen Data Rate, or 56 Gb/sec) InfiniBand Our old system Intel Nehalem processors and InfiniBand interconnect Here's the mpi info on the new system.: login4 >> mpif77 -v mpif77 for the Intel(R) MPI Library 4.1 for Linux* Copyright(C) 2003-2012, Intel Corporation. All rights reserved. ifort version 13.0.1 Any ideas why I'm having trouble reading in restart data on this new system? Thanks! --Mike From nek5000-users at lists.mcs.anl.gov Fri May 24 14:56:04 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 24 May 2013 22:56:04 +0300 Subject: [Nek5000-users] troubles with examples In-Reply-To: References: Message-ID: Hello everybody, I am a new nek5000 user. I have just successfully compiled the package (on my 64 bit ubuntu) and run the examples: turbChannel, vortex, turbJet. Now, although the executable seems to solve the problems (the display outputs look reasonable), the output files with *.fldxxxx etc contain only zeros (I can see that using postnek). Moreover, at the end of the run (vortex), at the summary, the output that appears on the display is as in the attachment (only zeros). Many thanks in advance, Barak Galanti -------------- next part -------------- 40021 U-PRES gmres: 1 5.8090E-16 1.0000E-07 7.9965E-16 0.0000E+00 0.0000E+00 40021 DNORM, DIVEX 9.6826759533351624E-015 5.8090008701096374E-016 40021 2.0010E+03 0.0000E+00 Fluid done 40021 2.001050E+03 -7.958699E-03 VMIN call outfld: ifpsco: F 40021 2.0010E+03 Write checkpoint: 40021 2.0010E+03 OPEN: r1854a.fld202 end of time-step loop runtime statistics: total time 9.9999999999999995E-008 inv3 time 161934 0.0000000000000000 0.0000000000000000 invc time 0 0.0000000000000000 0.0000000000000000 mltd time 605865 0.0000000000000000 0.0000000000000000 cdtp time 605865 0.0000000000000000 0.0000000000000000 eslv time 40021 0.0000000000000000 0.0000000000000000 pres time 40021 0.0000000000000000 0.0000000000000000 crsl time 41880 0.0000000000000000 0.0000000000000000 crsl min 0.0000000000000000 crsl max 0.0000000000000000 crsl avg 0.0000000000000000 hmhz time 6 0.0000000000000000 0.0000000000000000 spro time 40022 0.0000000000000000 0.0000000000000000 usbc time 40021 0.0000000000000000 0.0000000000000000 usbc min 0.0000000000000000 usbc max 0.0000000000000000 usb avg 0.0000000000000000 axhm time 888174 0.0000000000000000 0.0000000000000000 advc time 40021 0.0000000000000000 0.0000000000000000 vdss time 161935 0.0000000000000000 0.0000000000000000 vdss min 0.0000000000000000 vdss max 0.0000000000000000 vdss avg 0.0000000000000000 dsum time 893746 0.0000000000000000 0.0000000000000000 dsum min 0.0000000000000000 dsum max 0.0000000000000000 dsum avg 0.0000000000000000 dadd time 0 0.0000000000000000 0.0000000000000000 ddsl time 41880 0.0000000000000000 0.0000000000000000 solv time 41880 0.0000000000000000 0.0000000000000000 prep time 40022 0.0000000000000000 0.0000000000000000 # nid tusbc tdadd tcrsl tvdss tdsum tgop qqq F 0 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 qqq 1 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 qqq 2 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 qqq 3 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 qqq call exitt: dying ... backtrace(): obtained 5 stack frames. ./nek5000(print_stack_+0x18) [0x50e8f8] ./nek5000(exitt_+0x1d0) [0x5fa6a0] ./nek5000(main+0x3b) [0x41ae8b] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7fe09c09376d] ./nek5000() [0x41aebd] total elapsed time : 0.00000E+00 sec total solver time incl. I/O : 0.00000E+00 sec time/timestep : 0.00000E+00 sec CPU seconds/timestep/gridpt : 0.00000E+00 sec From nek5000-users at lists.mcs.anl.gov Fri May 24 19:34:15 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 24 May 2013 19:34:15 -0500 Subject: [Nek5000-users] Prenek and Genbox - Maketools problems In-Reply-To: References: Message-ID: Hi JP, I have update the nek5_svn/trunk/tools to reflect the shell script change and to fix the genbox bug. If you could update your tools and do a "./maketools clean; ./maketools all" things should be working better. I have not been able to replicate the prenek error, but the error message, : XIO: fatal IO error 11 (Resource temporarily unavailable) on X server ":0" after 153 requests (153 known processed) with 0 events remaining. Usually just means that X11 was closed in a non-standard way. If you are still having prenek issues, could you explain to me what isn't working, or what happens when you try to start a session? Thanks, Katie On Thu, May 23, 2013 at 4:35 PM, wrote: > Hi Katie, > > Yes thanks, the problem when compiling is solved. I imagined it was > something related to bash but it didn't cross my mind to check the makefile. > > Unfortunately the errors with genbox (when trying to output a .re2 file) > and prex (the errors I mentioned + interface does not work well) still > remain (even after re-making the tools). > > Thanks, > JP > > _______________________________________________ > 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 Sat May 25 12:42:03 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 25 May 2013 19:42:03 +0200 Subject: [Nek5000-users] Prenek and Genbox - Maketools problems Message-ID: Hi Katie, Thanks, genbox is creating the .re2 file without any errors now and you are right regrading the IO error.. it appears since I close prex by just closing the window. Regarding what's happening with PRENEK: in general, for 'PREX', it prints the following error every time when opening: 'I/O Error: No String Terminator sent to PRS' Then when I input a name for the session (after the prompt "Choose a Name for This Session:" ) the program does nothing. It doesn't take the session name and I can keep on typing text and pressing enter with no response. On the other hand, for 'PRETEX', it doesn't show the 'I/O Error: No String Terminator sent to PRS' at the beginning but gives: 'cp: cannot stat `/home/jpm/.nekdefaults': No such file or directory' It lets me input a session name and this time it accepts it and i manage to go through the menu options but when trying to 'read previous parameters' it gives 'Error reading parameters from file.' When I try the 'Type in new parameters' it lets me carry on but when I try to 'Build interactively' the following message appears: 'Error: Grid must be between 0 and 1 (fraction of Screen height). Screen gridding couldnt be changed drwobjs: 0' I then go through some stages, and manage to, for example, use the 'Import Mesh' but the mesh is not imported correctly and grey boxes appear (which I imagine should be clickable options) but there is nothing inside them. Other options seem to work partially but never successfully, it is as though there is something wrong with the output to the Nekton window. Sorry if the above is confusing but I tried to summarise what is happening. Thank you, JP -------------- next part -------------- An HTML attachment was scrubbed... URL: