From nek5000-users at lists.mcs.anl.gov Wed Mar 6 04:10:28 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 6 Mar 2013 10:10:28 +0000 Subject: [Nek5000-users] Visit reader for double precision f files In-Reply-To: References: Message-ID: Dear Neks, Reference to our previous question regarding reading double precision Nekton output file in Visit, we have tried to use the latest version of Visit, 2.6.1 However the problem is still there and visit cannot read the double precision Nekton files correctly. I was wondering if you could help us to solve this problem. With many thanks Reza ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Friday, November 16, 2012 4:04 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Visit reader for double precision f files Dear Neks, Reference to previous discussion (Sep.13th) about the support for the reading 64 bit files of nek5000 in VisIt, we have put up together a 3D cylinder as test case. For a double-precision format nek5000 dump file the 3D view and especially iso-contours are working fine whereas any 2D projection slice, or cut of the data is not working properly. In general operations considering the whole grid seem to work fine, but those related to a section of the grid such as box don't. This anomaly is happening regardless of choosing various pressure solver scheme (Pn_Pn/Pn_Pn-2) or including the grid data to be dumped in the file or not. I was wondering if you can help me with this issue. With many thanks Reza P.S. The 3D cylinder test-case located at the origin (0,0,0) of the coordinate system and extruded along the z-axis (perpendicular to the xy plane). The box extends from -15 to 25 in x direction, -9 to 9 in y direction and -2 to 2 in z directions. The mesh is constructed from the 2D cylinder in nek5000 repository. The number of elements is reduced, then extended in the z direction. An example of the dumped file can be found in the ftn: ftp://ftp.mech.kth.se/pub/pschlatt/nek5000 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 8 12:11:56 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 8 Mar 2013 12:11:56 -0600 Subject: [Nek5000-users] Impose inflow conditions from another simulation In-Reply-To: References: Message-ID: Hello, As a first step, here's a code snippet that would give you the xyz coordinates of the inlet (assuming there is only one inlet): do iel=1,nelv do ifc=1,2*ndim if (cbc(ifc,iel,1).eq.'v ') then call facind(kx1,kx2,ky1,ky2,kz1,kz2,nx1,ny1,nz1,ifc) do iz=kz1,kz2 do iy=ky1,ky2 do ix=kx1,kx2 x = xm1(ix,iy,iz,iel) y = ym1(ix,iy,iz,iel) z = zm1(ix,iy,iz,iel) ! Do whatever printing you want to do here enddo enddo enddo endif enddo enddo I don't think nek has any built-in routines for interpolating face data, but one could certainly build one using some of the functions from speclib.f. Josh On Wed, Feb 27, 2013 at 5:52 AM, wrote: > Hello nek5000-users,**** > > ** ** > > I have a data file obtained through a RANS simulation that I would like to > use as the inflow condition for my subsequent nek5000 simulation. **** > > ** ** > > May I know whether there is an efficient subroutine which allows me to > interpolate the RANS data onto the spectral-element mesh or, at least, > allows me to dump out the nodal points at the inlet so that I can perform > the interpolation and assignment? **** > > ** ** > > I will be performing a parallel simulation involving 300000 elements. > Hence I will be grateful if someone could provide me with an efficient > method.**** > > ** ** > > Thanks in advance.**** > > ** ** > > *Ng Jee Hann (Mr.)***** > > *PhD Student.* > > Department of Mechanical Engineering,**** > > National University of Singapore,**** > > 9 Engineering Drive 1, **** > > Singapore 117576.**** > > ** ** > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -- Josh Camp "All that is necessary for the triumph of evil is that good men do nothing" -- Edmund Burke -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Mar 12 05:36:36 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 12 Mar 2013 16:06:36 +0530 Subject: [Nek5000-users] Question about "taylor" example Message-ID: Hello In the example "taylor", I notice that the radii r0, r1 are set at line no. 191, 192 here http://trac.mcs.anl.gov/projects/nek5/browser/examples/taylor/taylor.usr but then they are modified at line no. 214, 215. I did not understand the reason for this. Changing r0, r1 will change the parameters "a" and "b". Thanks praveen -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Mar 12 07:22:28 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 12 Mar 2013 07:22:28 -0500 (CDT) Subject: [Nek5000-users] =?utf-8?q?Question_about_=22taylor=22_example?= In-Reply-To: References: Message-ID: Good question... It seems to be giving spectral accuracy in any case... I can't recall the details of whether the a & b influence the result or not. We'll check into it. Thank you Praveen. Paul On Tue, 12 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: > Hello > > In the example "taylor", I notice that the radii r0, r1 are set at line no. > 191, 192 here > > http://trac.mcs.anl.gov/projects/nek5/browser/examples/taylor/taylor.usr > > but then they are modified at line no. 214, 215. I did not understand the > reason for this. Changing r0, r1 will change the parameters "a" and "b". > > Thanks > praveen > From nek5000-users at lists.mcs.anl.gov Tue Mar 12 08:36:47 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 12 Mar 2013 19:06:47 +0530 Subject: [Nek5000-users] Question about "taylor" example In-Reply-To: References: Message-ID: You are right. It will still give correct solution. Thanks praveen On Tue, Mar 12, 2013 at 5:52 PM, wrote: > > Good question... > > It seems to be giving spectral accuracy in any case... > > I can't recall the details of whether the a & b > influence the result or not. We'll check into it. > > Thank you Praveen. > > Paul > > > > On Tue, 12 Mar 2013, nek5000-users at lists.mcs.anl.**govwrote: > > Hello >> >> In the example "taylor", I notice that the radii r0, r1 are set at line >> no. >> 191, 192 here >> >> http://trac.mcs.anl.gov/**projects/nek5/browser/** >> examples/taylor/taylor.usr >> >> but then they are modified at line no. 214, 215. I did not understand the >> reason for this. Changing r0, r1 will change the parameters "a" and "b". >> >> Thanks >> praveen >> >> ______________________________**_________________ > 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 Mar 20 08:10:44 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 20 Mar 2013 14:10:44 +0100 Subject: [Nek5000-users] trouble with visit Message-ID: Hi Neks, I am facing problems with the visualization in visit. The output of the three scalar fields uzt, epst, epsv is done is seen in the following line from my usr file. Here, I wrote the data into four files (see further below). I also attach the visit script !-------usr file------------------------------------------------- tiny=1.e-16 do i=1,n epst(i)=log(epst(i)+tiny) epsv(i)=log(epsv(i)+tiny) enddo !-------No pressure field, no scalar output ifpo=.false. ifto=.false. call outpost2( uzt,epst,epsv,pr,t,0,'eps') ifpo=.true. ifto=.true. !-------Visit script------------------------------------------------ NEK5000 version: 1.0 filetemplate: epsG1_64%d.f%05d firsttimestep: 1 numtimesteps: 1 !-------the four files that have to be load into visit and which make up one snapshot-------------- -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:03 epsG1_640.f00001 -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:09 epsG1_641.f00001 -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:16 epsG1_642.f00001 -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:22 epsG1_643.f00001 -rw-r----- 1 josc1234 linux 87 20. M?r 13:37 vis.nek5000 !-------This is the error message in visit--------------------------------------- The compute engine running on makalu51.rz.tu-ilmenau.de has exited abnormally. Shortly thereafter, the following occured... The Pseudocolor plot of "y_velocity" for the file "/usr/wrk/people4/josc1234/nek5_visit/r095_Lx1_12_Ra1e8/vis.nek5000" could not be generated by the compute engine on host "localhost". My questions: Could it be that the graphics output should be in single precision? I saw that the people at KTH did have similar trouble. If yes, how can I switch to single precision in the usr file output? For smaller grid it worked. Thanks in advance, Joerg. From nek5000-users at lists.mcs.anl.gov Wed Mar 20 08:43:54 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 20 Mar 2013 08:43:54 -0500 (CDT) Subject: [Nek5000-users] trouble with visit In-Reply-To: References: Message-ID: Hi Joerg, Normally the output is indeed in single precision. It's not clear to me the double-precision + visit is working - but I've been a bit out of the loop on this. Paul On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: > Hi Neks, > > I am facing problems with the visualization in visit. > The output of the three scalar fields uzt, epst, epsv > is done is seen in the following line from my usr file. > > Here, I wrote the data into four files (see further below). > I also attach the visit script > > !-------usr file------------------------------------------------- > tiny=1.e-16 > do i=1,n > epst(i)=log(epst(i)+tiny) > epsv(i)=log(epsv(i)+tiny) > enddo > > !-------No pressure field, no scalar output > ifpo=.false. > ifto=.false. > > call outpost2( uzt,epst,epsv,pr,t,0,'eps') > > ifpo=.true. > ifto=.true. > > > > !-------Visit script------------------------------------------------ > NEK5000 > version: 1.0 > filetemplate: epsG1_64%d.f%05d > firsttimestep: 1 > numtimesteps: 1 > > > > !-------the four files that have to be load into visit and which make up one snapshot-------------- > -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:03 epsG1_640.f00001 > -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:09 epsG1_641.f00001 > -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:16 epsG1_642.f00001 > -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:22 epsG1_643.f00001 > -rw-r----- 1 josc1234 linux 87 20. M?r 13:37 vis.nek5000 > > > > !-------This is the error message in visit--------------------------------------- > The compute engine running on makalu51.rz.tu-ilmenau.de has exited abnormally. > > Shortly thereafter, the following occured... > > The Pseudocolor plot of "y_velocity" for the file "/usr/wrk/people4/josc1234/nek5_visit/r095_Lx1_12_Ra1e8/vis.nek5000" could not be generated by the compute engine on host "localhost". > > > > My questions: > > Could it be that the graphics output should be in single precision? > I saw that the people at KTH did have similar trouble. > If yes, how can I switch to single precision in the usr file output? > For smaller grid it worked. > > Thanks in advance, Joerg. > > > _______________________________________________ > 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 Mar 20 08:45:03 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 20 Mar 2013 08:45:03 -0500 Subject: [Nek5000-users] trouble with visit In-Reply-To: References: Message-ID: Hi Joerg, What's your header (output of: head -1 blah0.f?????) Justin On Wed, 20 Mar 2013 14:10:44 +0100 nek5000-users at lists.mcs.anl.gov wrote: > Hi Neks, > > I am facing problems with the visualization in visit. > The output of the three scalar fields uzt, epst, epsv > is done is seen in the following line from my usr file. > > Here, I wrote the data into four files (see further below). > I also attach the visit script > > !-------usr file------------------------------------------------- > tiny=1.e-16 > do i=1,n > epst(i)=log(epst(i)+tiny) > epsv(i)=log(epsv(i)+tiny) > enddo > > !-------No pressure field, no scalar output > ifpo=.false. > ifto=.false. > > call outpost2( uzt,epst,epsv,pr,t,0,'eps') > > ifpo=.true. > ifto=.true. > > > > !-------Visit script------------------------------------------------ > NEK5000 > version: 1.0 > filetemplate: epsG1_64%d.f%05d > firsttimestep: 1 > numtimesteps: 1 > > > > !-------the four files that have to be load into visit and which make > up one snapshot-------------- -rw-r--r-- 1 josc1234 linux 2657536136 > 27. Feb 08:03 epsG1_640.f00001 -rw-r--r-- 1 josc1234 linux 2657536136 > 27. Feb 08:09 epsG1_641.f00001 -rw-r--r-- 1 josc1234 linux 2657536136 > 27. Feb 08:16 epsG1_642.f00001 -rw-r--r-- 1 josc1234 linux 2657536136 > 27. Feb 08:22 epsG1_643.f00001 -rw-r----- 1 josc1234 linux 87 > 20. M__r 13:37 vis.nek5000 > > > > !-------This is the error message in > visit--------------------------------------- The compute engine > running on makalu51.rz.tu-ilmenau.de has exited abnormally. > > Shortly thereafter, the following occured... > > The Pseudocolor plot of "y_velocity" for the file > "/usr/wrk/people4/josc1234/nek5_visit/r095_Lx1_12_Ra1e8/vis.nek5000" > could not be generated by the compute engine on host "localhost". > > > > My questions: > > Could it be that the graphics output should be in single precision? > I saw that the people at KTH did have similar trouble. > If yes, how can I switch to single precision in the usr file output? > For smaller grid it worked. > > Thanks in advance, Joerg. > > > _______________________________________________ > 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 Mar 20 08:46:29 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 20 Mar 2013 14:46:29 +0100 Subject: [Nek5000-users] trouble with visit In-Reply-To: References: Message-ID: Hi Paul, how can I set up the single precision output? best regards, Joerg. > Hi Joerg, > > Normally the output is indeed in single precision. > It's not clear to me the double-precision + visit > is working - but I've been a bit out of the loop > on this. > > Paul > > > On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: > >> Hi Neks, >> >> I am facing problems with the visualization in visit. >> The output of the three scalar fields uzt, epst, epsv >> is done is seen in the following line from my usr file. >> >> Here, I wrote the data into four files (see further below). >> I also attach the visit script >> >> !-------usr file------------------------------------------------- >> tiny=1.e-16 >> do i=1,n >> epst(i)=log(epst(i)+tiny) >> epsv(i)=log(epsv(i)+tiny) >> enddo >> >> !-------No pressure field, no scalar output >> ifpo=.false. >> ifto=.false. >> >> call outpost2( uzt,epst,epsv,pr,t,0,'eps') >> >> ifpo=.true. >> ifto=.true. >> >> >> >> !-------Visit script------------------------------------------------ >> NEK5000 >> version: 1.0 >> filetemplate: epsG1_64%d.f%05d >> firsttimestep: 1 >> numtimesteps: 1 >> >> >> >> !-------the four files that have to be load into visit and which make up one snapshot-------------- >> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:03 epsG1_640.f00001 >> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:09 epsG1_641.f00001 >> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:16 epsG1_642.f00001 >> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:22 epsG1_643.f00001 >> -rw-r----- 1 josc1234 linux 87 20. M?r 13:37 vis.nek5000 >> >> >> >> !-------This is the error message in visit--------------------------------------- >> The compute engine running on makalu51.rz.tu-ilmenau.de has exited abnormally. >> >> Shortly thereafter, the following occured... >> >> The Pseudocolor plot of "y_velocity" for the file "/usr/wrk/people4/josc1234/nek5_visit/r095_Lx1_12_Ra1e8/vis.nek5000" could not be generated by the compute engine on host "localhost". >> >> >> >> My questions: >> >> Could it be that the graphics output should be in single precision? >> I saw that the people at KTH did have similar trouble. >> If yes, how can I switch to single precision in the usr file output? >> For smaller grid it worked. >> >> Thanks in advance, Joerg. >> >> >> _______________________________________________ >> 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 Mar 20 08:47:20 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 20 Mar 2013 08:47:20 -0500 (CDT) Subject: [Nek5000-users] trouble with visit In-Reply-To: References: Message-ID: It looks like setting p63=0 should take care of that... Paul On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: > Hi Paul, how can I set up the single precision output? best regards, Joerg. > Hi Joerg, > > Normally the output is indeed in single precision. > It's not clear to me the double-precision + visit > is working - but I've been a bit out of the loop > on this. > > Paul > > > On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: > >> Hi Neks, >> >> I am facing problems with the visualization in visit. >> The output of the three scalar fields uzt, epst, epsv >> is done is seen in the following line from my usr file. >> >> Here, I wrote the data into four files (see further below). >> I also attach the visit script >> >> !-------usr file------------------------------------------------- >> tiny=1.e-16 >> do i=1,n >> epst(i)=log(epst(i)+tiny) >> epsv(i)=log(epsv(i)+tiny) >> enddo >> >> !-------No pressure field, no scalar output >> ifpo=.false. >> ifto=.false. >> >> call outpost2( uzt,epst,epsv,pr,t,0,'eps') >> >> ifpo=.true. >> ifto=.true. >> >> >> >> !-------Visit script------------------------------------------------ >> NEK5000 >> version: 1.0 >> filetemplate: epsG1_64%d.f%05d >> firsttimestep: 1 >> numtimesteps: 1 >> >> >> >> !-------the four files that have to be load into visit and which make up one snapshot-------------- >> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:03 epsG1_640.f00001 >> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:09 epsG1_641.f00001 >> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:16 epsG1_642.f00001 >> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:22 epsG1_643.f00001 >> -rw-r----- 1 josc1234 linux 87 20. M?r 13:37 vis.nek5000 >> >> >> >> !-------This is the error message in visit--------------------------------------- >> The compute engine running on makalu51.rz.tu-ilmenau.de has exited abnormally. >> >> Shortly thereafter, the following occured... >> >> The Pseudocolor plot of "y_velocity" for the file "/usr/wrk/people4/josc1234/nek5_visit/r095_Lx1_12_Ra1e8/vis.nek5000" could not be generated by the compute engine on host "localhost". >> >> >> >> My questions: >> >> Could it be that the graphics output should be in single precision? >> I saw that the people at KTH did have similar trouble. >> If yes, how can I switch to single precision in the usr file output? >> For smaller grid it worked. >> >> Thanks in advance, Joerg. >> >> >> _______________________________________________ >> 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 Mar 20 10:03:10 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 20 Mar 2013 16:03:10 +0100 Subject: [Nek5000-users] trouble with visit In-Reply-To: References: Message-ID: p63 is set to zero and it still does not work Joerg Am 20.03.2013 um 14:47 schrieb nek5000-users at lists.mcs.anl.gov: > > It looks like setting p63=0 should take care of that... > > Paul > > > On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: > >> Hi Paul, > > how can I set up the single precision output? > > best regards, Joerg. > >> Hi Joerg, >> Normally the output is indeed in single precision. >> It's not clear to me the double-precision + visit >> is working - but I've been a bit out of the loop >> on this. >> Paul >> On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: >>> Hi Neks, >>> >>> I am facing problems with the visualization in visit. >>> The output of the three scalar fields uzt, epst, epsv >>> is done is seen in the following line from my usr file. >>> >>> Here, I wrote the data into four files (see further below). >>> I also attach the visit script >>> >>> !-------usr file------------------------------------------------- >>> tiny=1.e-16 >>> do i=1,n >>> epst(i)=log(epst(i)+tiny) >>> epsv(i)=log(epsv(i)+tiny) >>> enddo >>> >>> !-------No pressure field, no scalar output >>> ifpo=.false. >>> ifto=.false. >>> >>> call outpost2( uzt,epst,epsv,pr,t,0,'eps') >>> >>> ifpo=.true. >>> ifto=.true. >>> >>> >>> >>> !-------Visit script------------------------------------------------ >>> NEK5000 >>> version: 1.0 >>> filetemplate: epsG1_64%d.f%05d >>> firsttimestep: 1 >>> numtimesteps: 1 >>> >>> >>> >>> !-------the four files that have to be load into visit and which make up one snapshot-------------- >>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:03 epsG1_640.f00001 >>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:09 epsG1_641.f00001 >>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:16 epsG1_642.f00001 >>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:22 epsG1_643.f00001 >>> -rw-r----- 1 josc1234 linux 87 20. M?r 13:37 vis.nek5000 >>> >>> >>> >>> !-------This is the error message in visit--------------------------------------- >>> The compute engine running on makalu51.rz.tu-ilmenau.de has exited abnormally. >>> >>> Shortly thereafter, the following occured... >>> >>> The Pseudocolor plot of "y_velocity" for the file "/usr/wrk/people4/josc1234/nek5_visit/r095_Lx1_12_Ra1e8/vis.nek5000" could not be generated by the compute engine on host "localhost". >>> >>> >>> >>> My questions: >>> >>> Could it be that the graphics output should be in single precision? >>> I saw that the people at KTH did have similar trouble. >>> If yes, how can I switch to single precision in the usr file output? >>> For smaller grid it worked. >>> >>> Thanks in advance, Joerg. >>> >>> >>> _______________________________________________ >>> 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 Wed Mar 20 10:23:35 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 20 Mar 2013 10:23:35 -0500 (CDT) Subject: [Nek5000-users] trouble with visit In-Reply-To: Message-ID: Hi Joerg, Did you try Justin's suggestion of looking at your header? It probably already is 32-bit ? ? (This would normally be the case.) Perhaps the output data is corrupted, e.g., nans or whatever...? Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Wednesday, March 20, 2013 10:03:10 AM Subject: Re: [Nek5000-users] trouble with visit p63 is set to zero and it still does not work Joerg Am 20.03.2013 um 14:47 schrieb nek5000-users at lists.mcs.anl.gov: > > It looks like setting p63=0 should take care of that... > > Paul > > > On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: > >> Hi Paul, > > how can I set up the single precision output? > > best regards, Joerg. > >> Hi Joerg, >> Normally the output is indeed in single precision. >> It's not clear to me the double-precision + visit >> is working - but I've been a bit out of the loop >> on this. >> Paul >> On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: >>> Hi Neks, >>> >>> I am facing problems with the visualization in visit. >>> The output of the three scalar fields uzt, epst, epsv >>> is done is seen in the following line from my usr file. >>> >>> Here, I wrote the data into four files (see further below). >>> I also attach the visit ?script >>> >>> !-------usr file------------------------------------------------- >>> ? ? ? tiny=1.e-16 >>> ? ? ? do i=1,n >>> ? ? ? ?epst(i)=log(epst(i)+tiny) >>> ? ? ? ?epsv(i)=log(epsv(i)+tiny) >>> ? ? ? enddo >>> >>> !-------No pressure field, no scalar output >>> ? ? ? ifpo=.false. >>> ? ? ? ifto=.false. >>> >>> ? ? ? call outpost2( uzt,epst,epsv,pr,t,0,'eps') >>> >>> ? ? ? ifpo=.true. >>> ? ? ? ifto=.true. >>> >>> >>> >>> !-------Visit script------------------------------------------------ >>> NEK5000 >>> version: 1.0 >>> filetemplate: epsG1_64%d.f%05d >>> firsttimestep: 1 >>> numtimesteps: 1 >>> >>> >>> >>> !-------the four files that have to be load into visit and which make up one snapshot-------------- >>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:03 epsG1_640.f00001 >>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:09 epsG1_641.f00001 >>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:16 epsG1_642.f00001 >>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:22 epsG1_643.f00001 >>> -rw-r----- 1 josc1234 linux ? ? ? ? 87 20. M?r 13:37 vis.nek5000 >>> >>> >>> >>> !-------This is the error message in visit--------------------------------------- >>> The compute engine running on makalu51.rz.tu-ilmenau.de has exited abnormally. >>> >>> Shortly thereafter, the following occured... >>> >>> The Pseudocolor plot of "y_velocity" for the file "/usr/wrk/people4/josc1234/nek5_visit/r095_Lx1_12_Ra1e8/vis.nek5000" could not be generated by the compute engine on host "localhost". >>> >>> >>> >>> My questions: >>> >>> Could it be that the graphics output should be in single precision? >>> I saw that the people at KTH did have similar trouble. >>> If yes, how can I switch to single precision in the usr file output? >>> For smaller grid it worked. >>> >>> Thanks in advance, Joerg. >>> >>> >>> _______________________________________________ >>> 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 Wed Mar 20 10:42:04 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 20 Mar 2013 16:42:04 +0100 Subject: [Nek5000-users] trouble with visit In-Reply-To: References: Message-ID: Hi Paul, I didn't understand what Justin meant. The first line in all output files looks like this: #std 4 12 12 12 64000 256000 .2165378385933E+03 5000 2 4 XU Thanks Joerg. > Hi Joerg, > > Did you try Justin's suggestion of looking at your header? > It probably already is 32-bit ? ? (This would normally be > the case.) > > Perhaps the output data is corrupted, e.g., nans or whatever...? > > Paul > > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Sent: Wednesday, March 20, 2013 10:03:10 AM > Subject: Re: [Nek5000-users] trouble with visit > > p63 is set to zero and it still does not work > > Joerg > > Am 20.03.2013 um 14:47 schrieb nek5000-users at lists.mcs.anl.gov: > >> >> It looks like setting p63=0 should take care of that... >> >> Paul >> >> >> On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: >> >>> Hi Paul, >> >> how can I set up the single precision output? >> >> best regards, Joerg. >> >>> Hi Joerg, >>> Normally the output is indeed in single precision. >>> It's not clear to me the double-precision + visit >>> is working - but I've been a bit out of the loop >>> on this. >>> Paul >>> On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: >>>> Hi Neks, >>>> >>>> I am facing problems with the visualization in visit. >>>> The output of the three scalar fields uzt, epst, epsv >>>> is done is seen in the following line from my usr file. >>>> >>>> Here, I wrote the data into four files (see further below). >>>> I also attach the visit ?script >>>> >>>> !-------usr file------------------------------------------------- >>>> ? ? ? tiny=1.e-16 >>>> ? ? ? do i=1,n >>>> ? ? ? ?epst(i)=log(epst(i)+tiny) >>>> ? ? ? ?epsv(i)=log(epsv(i)+tiny) >>>> ? ? ? enddo >>>> >>>> !-------No pressure field, no scalar output >>>> ? ? ? ifpo=.false. >>>> ? ? ? ifto=.false. >>>> >>>> ? ? ? call outpost2( uzt,epst,epsv,pr,t,0,'eps') >>>> >>>> ? ? ? ifpo=.true. >>>> ? ? ? ifto=.true. >>>> >>>> >>>> >>>> !-------Visit script------------------------------------------------ >>>> NEK5000 >>>> version: 1.0 >>>> filetemplate: epsG1_64%d.f%05d >>>> firsttimestep: 1 >>>> numtimesteps: 1 >>>> >>>> >>>> >>>> !-------the four files that have to be load into visit and which make up one snapshot-------------- >>>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:03 epsG1_640.f00001 >>>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:09 epsG1_641.f00001 >>>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:16 epsG1_642.f00001 >>>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:22 epsG1_643.f00001 >>>> -rw-r----- 1 josc1234 linux ? ? ? ? 87 20. M?r 13:37 vis.nek5000 >>>> >>>> >>>> >>>> !-------This is the error message in visit--------------------------------------- >>>> The compute engine running on makalu51.rz.tu-ilmenau.de has exited abnormally. >>>> >>>> Shortly thereafter, the following occured... >>>> >>>> The Pseudocolor plot of "y_velocity" for the file "/usr/wrk/people4/josc1234/nek5_visit/r095_Lx1_12_Ra1e8/vis.nek5000" could not be generated by the compute engine on host "localhost". >>>> >>>> >>>> >>>> My questions: >>>> >>>> Could it be that the graphics output should be in single precision? >>>> I saw that the people at KTH did have similar trouble. >>>> If yes, how can I switch to single precision in the usr file output? >>>> For smaller grid it worked. >>>> >>>> Thanks in advance, Joerg. >>>> >>>> >>>> _______________________________________________ >>>> 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 > _______________________________________________ > 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 Mar 20 10:49:49 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 20 Mar 2013 10:49:49 -0500 (CDT) Subject: [Nek5000-users] trouble with visit In-Reply-To: References: Message-ID: Hi Joerg, The first " 4 " indicates that the data is output in 4-byte (32-bit) format. My guess is that there might be a problem with the raw data in the fields that are being written. For example, what is the sign of epst() ? Is it guaranteed to be positive ? do i=1,n epst(i)=log(epst(i)+tiny) epsv(i)=log(epsv(i)+tiny) enddo Paul On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: > Hi Paul, I didn't understand what Justin meant. The first line in all output files looks like this: #std 4 12 12 12 64000 256000 .2165378385933E+03 5000 2 4 XU Thanks Joerg. > Hi Joerg, > > Did you try Justin's suggestion of looking at your header? > It probably already is 32-bit ? ?? (This would normally be > the case.) > > Perhaps the output data is corrupted, e.g., nans or whatever...? > > Paul > > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Sent: Wednesday, March 20, 2013 10:03:10 AM > Subject: Re: [Nek5000-users] trouble with visit > > p63 is set to zero and it still does not work > > Joerg > > Am 20.03.2013 um 14:47 schrieb nek5000-users at lists.mcs.anl.gov: > >> >> It looks like setting p63=0 should take care of that... >> >> Paul >> >> >> On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: >> >>> Hi Paul, >> >> how can I set up the single precision output? >> >> best regards, Joerg. >> >>> Hi Joerg, >>> Normally the output is indeed in single precision. >>> It's not clear to me the double-precision + visit >>> is working - but I've been a bit out of the loop >>> on this. >>> Paul >>> On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: >>>> Hi Neks, >>>> >>>> I am facing problems with the visualization in visit. >>>> The output of the three scalar fields uzt, epst, epsv >>>> is done is seen in the following line from my usr file. >>>> >>>> Here, I wrote the data into four files (see further below). >>>> I also attach the visit ??script >>>> >>>> !-------usr file------------------------------------------------- >>>> ?? ?? ?? tiny=1.e-16 >>>> ?? ?? ?? do i=1,n >>>> ?? ?? ?? ??epst(i)=log(epst(i)+tiny) >>>> ?? ?? ?? ??epsv(i)=log(epsv(i)+tiny) >>>> ?? ?? ?? enddo >>>> >>>> !-------No pressure field, no scalar output >>>> ?? ?? ?? ifpo=.false. >>>> ?? ?? ?? ifto=.false. >>>> >>>> ?? ?? ?? call outpost2( uzt,epst,epsv,pr,t,0,'eps') >>>> >>>> ?? ?? ?? ifpo=.true. >>>> ?? ?? ?? ifto=.true. >>>> >>>> >>>> >>>> !-------Visit script------------------------------------------------ >>>> NEK5000 >>>> version: 1.0 >>>> filetemplate: epsG1_64%d.f%05d >>>> firsttimestep: 1 >>>> numtimesteps: 1 >>>> >>>> >>>> >>>> !-------the four files that have to be load into visit and which make up one snapshot-------------- >>>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:03 epsG1_640.f00001 >>>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:09 epsG1_641.f00001 >>>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:16 epsG1_642.f00001 >>>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:22 epsG1_643.f00001 >>>> -rw-r----- 1 josc1234 linux ?? ?? ?? ?? 87 20. M??r 13:37 vis.nek5000 >>>> >>>> >>>> >>>> !-------This is the error message in visit--------------------------------------- >>>> The compute engine running on makalu51.rz.tu-ilmenau.de has exited abnormally. >>>> >>>> Shortly thereafter, the following occured... >>>> >>>> The Pseudocolor plot of "y_velocity" for the file "/usr/wrk/people4/josc1234/nek5_visit/r095_Lx1_12_Ra1e8/vis.nek5000" could not be generated by the compute engine on host "localhost". >>>> >>>> >>>> >>>> My questions: >>>> >>>> Could it be that the graphics output should be in single precision? >>>> I saw that the people at KTH did have similar trouble. >>>> If yes, how can I switch to single precision in the usr file output? >>>> For smaller grid it worked. >>>> >>>> Thanks in advance, Joerg. >>>> >>>> >>>> _______________________________________________ >>>> 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 > _______________________________________________ > 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 Mar 20 10:58:08 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 20 Mar 2013 16:58:08 +0100 Subject: [Nek5000-users] trouble with visit In-Reply-To: References: Message-ID: Hi Paul, I will check. The same worked for smaller grids. epst and epsv are positive definite. It is probably a visit problem. Best regards, Joerg. Am 20.03.2013 um 16:49 schrieb nek5000-users at lists.mcs.anl.gov: > > Hi Joerg, > > The first " 4 " indicates that the data is output in 4-byte (32-bit) > format. > > My guess is that there might be a problem with the raw data > in the fields that are being written. For example, what is > the sign of epst() ? Is it guaranteed to be positive ? > > do i=1,n > epst(i)=log(epst(i)+tiny) > epsv(i)=log(epsv(i)+tiny) > enddo > > Paul > > > On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: > >> Hi Paul, > > I didn't understand what Justin meant. > The first line in all output files looks like this: > > #std 4 12 12 12 64000 256000 .2165378385933E+03 5000 > 2 4 XU > > Thanks Joerg. > > > > > > >> Hi Joerg, >> Did you try Justin's suggestion of looking at your header? >> It probably already is 32-bit ? ? (This would normally be >> the case.) >> Perhaps the output data is corrupted, e.g., nans or whatever...? >> Paul >> ----- Original Message ----- >> From: nek5000-users at lists.mcs.anl.gov >> To: nek5000-users at lists.mcs.anl.gov >> Sent: Wednesday, March 20, 2013 10:03:10 AM >> Subject: Re: [Nek5000-users] trouble with visit >> p63 is set to zero and it still does not work >> Joerg >> Am 20.03.2013 um 14:47 schrieb nek5000-users at lists.mcs.anl.gov: >>> >>> It looks like setting p63=0 should take care of that... >>> >>> Paul >>> >>> >>> On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: >>> >>>> Hi Paul, >>> >>> how can I set up the single precision output? >>> >>> best regards, Joerg. >>> >>>> Hi Joerg, >>>> Normally the output is indeed in single precision. >>>> It's not clear to me the double-precision + visit >>>> is working - but I've been a bit out of the loop >>>> on this. >>>> Paul >>>> On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: >>>>> Hi Neks, >>>>> >>>>> I am facing problems with the visualization in visit. >>>>> The output of the three scalar fields uzt, epst, epsv >>>>> is done is seen in the following line from my usr file. >>>>> >>>>> Here, I wrote the data into four files (see further below). >>>>> I also attach the visit ? script >>>>> >>>>> !-------usr file------------------------------------------------- >>>>> ? ? ? tiny=1.e-16 >>>>> ? ? ? do i=1,n >>>>> ? ? ? ? epst(i)=log(epst(i)+tiny) >>>>> ? ? ? ? epsv(i)=log(epsv(i)+tiny) >>>>> ? ? ? enddo >>>>> >>>>> !-------No pressure field, no scalar output >>>>> ? ? ? ifpo=.false. >>>>> ? ? ? ifto=.false. >>>>> >>>>> ? ? ? call outpost2( uzt,epst,epsv,pr,t,0,'eps') >>>>> >>>>> ? ? ? ifpo=.true. >>>>> ? ? ? ifto=.true. >>>>> >>>>> >>>>> >>>>> !-------Visit script------------------------------------------------ >>>>> NEK5000 >>>>> version: 1.0 >>>>> filetemplate: epsG1_64%d.f%05d >>>>> firsttimestep: 1 >>>>> numtimesteps: 1 >>>>> >>>>> >>>>> >>>>> !-------the four files that have to be load into visit and which make up one snapshot-------------- >>>>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:03 epsG1_640.f00001 >>>>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:09 epsG1_641.f00001 >>>>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:16 epsG1_642.f00001 >>>>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:22 epsG1_643.f00001 >>>>> -rw-r----- 1 josc1234 linux ? ? ? ? 87 20. M??r 13:37 vis.nek5000 >>>>> >>>>> >>>>> >>>>> !-------This is the error message in visit--------------------------------------- >>>>> The compute engine running on makalu51.rz.tu-ilmenau.de has exited abnormally. >>>>> >>>>> Shortly thereafter, the following occured... >>>>> >>>>> The Pseudocolor plot of "y_velocity" for the file "/usr/wrk/people4/josc1234/nek5_visit/r095_Lx1_12_Ra1e8/vis.nek5000" could not be generated by the compute engine on host "localhost". >>>>> >>>>> >>>>> >>>>> My questions: >>>>> >>>>> Could it be that the graphics output should be in single precision? >>>>> I saw that the people at KTH did have similar trouble. >>>>> If yes, how can I switch to single precision in the usr file output? >>>>> For smaller grid it worked. >>>>> >>>>> Thanks in advance, Joerg. >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >> _______________________________________________ >> 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 Wed Mar 20 11:01:43 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 20 Mar 2013 11:01:43 -0500 Subject: [Nek5000-users] trouble with visit In-Reply-To: References: Message-ID: Just wondering what this reader is doing when you have the same extension .00001 for all four files..would f%05d still work? I imagine , at least, that it will have problem looping over your files filetemplate: epsG1_64%d.f%05d firsttimestep: 1 numtimesteps: 1 Ammar On Mar 20, 2013, at 10:58 AM, nek5000-users at lists.mcs.anl.gov wrote: > Hi Paul, > > I will check. The same worked for smaller grids. > epst and epsv are positive definite. > It is probably a visit problem. > > Best regards, Joerg. > > > > > Am 20.03.2013 um 16:49 schrieb nek5000-users at lists.mcs.anl.gov: > >> >> Hi Joerg, >> >> The first " 4 " indicates that the data is output in 4-byte (32-bit) >> format. >> >> My guess is that there might be a problem with the raw data >> in the fields that are being written. For example, what is >> the sign of epst() ? Is it guaranteed to be positive ? >> >> do i=1,n >> epst(i)=log(epst(i)+tiny) >> epsv(i)=log(epsv(i)+tiny) >> enddo >> >> Paul >> >> >> On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: >> >>> Hi Paul, >> >> I didn't understand what Justin meant. >> The first line in all output files looks like this: >> >> #std 4 12 12 12 64000 256000 .2165378385933E+03 5000 >> 2 4 XU >> >> Thanks Joerg. >> >> >> >> >> >> >>> Hi Joerg, >>> Did you try Justin's suggestion of looking at your header? >>> It probably already is 32-bit ? ? (This would normally be >>> the case.) >>> Perhaps the output data is corrupted, e.g., nans or whatever...? >>> Paul >>> ----- Original Message ----- >>> From: nek5000-users at lists.mcs.anl.gov >>> To: nek5000-users at lists.mcs.anl.gov >>> Sent: Wednesday, March 20, 2013 10:03:10 AM >>> Subject: Re: [Nek5000-users] trouble with visit >>> p63 is set to zero and it still does not work >>> Joerg >>> Am 20.03.2013 um 14:47 schrieb nek5000-users at lists.mcs.anl.gov: >>>> >>>> It looks like setting p63=0 should take care of that... >>>> >>>> Paul >>>> >>>> >>>> On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: >>>> >>>>> Hi Paul, >>>> >>>> how can I set up the single precision output? >>>> >>>> best regards, Joerg. >>>> >>>>> Hi Joerg, >>>>> Normally the output is indeed in single precision. >>>>> It's not clear to me the double-precision + visit >>>>> is working - but I've been a bit out of the loop >>>>> on this. >>>>> Paul >>>>> On Wed, 20 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: >>>>>> Hi Neks, >>>>>> >>>>>> I am facing problems with the visualization in visit. >>>>>> The output of the three scalar fields uzt, epst, epsv >>>>>> is done is seen in the following line from my usr file. >>>>>> >>>>>> Here, I wrote the data into four files (see further below). >>>>>> I also attach the visit ? script >>>>>> >>>>>> !-------usr file------------------------------------------------- >>>>>> ? ? ? tiny=1.e-16 >>>>>> ? ? ? do i=1,n >>>>>> ? ? ? ? epst(i)=log(epst(i)+tiny) >>>>>> ? ? ? ? epsv(i)=log(epsv(i)+tiny) >>>>>> ? ? ? enddo >>>>>> >>>>>> !-------No pressure field, no scalar output >>>>>> ? ? ? ifpo=.false. >>>>>> ? ? ? ifto=.false. >>>>>> >>>>>> ? ? ? call outpost2( uzt,epst,epsv,pr,t,0,'eps') >>>>>> >>>>>> ? ? ? ifpo=.true. >>>>>> ? ? ? ifto=.true. >>>>>> >>>>>> >>>>>> >>>>>> !-------Visit script------------------------------------------------ >>>>>> NEK5000 >>>>>> version: 1.0 >>>>>> filetemplate: epsG1_64%d.f%05d >>>>>> firsttimestep: 1 >>>>>> numtimesteps: 1 >>>>>> >>>>>> >>>>>> >>>>>> !-------the four files that have to be load into visit and which make up one snapshot-------------- >>>>>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:03 epsG1_640.f00001 >>>>>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:09 epsG1_641.f00001 >>>>>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:16 epsG1_642.f00001 >>>>>> -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:22 epsG1_643.f00001 >>>>>> -rw-r----- 1 josc1234 linux ? ? ? ? 87 20. M??r 13:37 vis.nek5000 >>>>>> >>>>>> >>>>>> >>>>>> !-------This is the error message in visit--------------------------------------- >>>>>> The compute engine running on makalu51.rz.tu-ilmenau.de has exited abnormally. >>>>>> >>>>>> Shortly thereafter, the following occured... >>>>>> >>>>>> The Pseudocolor plot of "y_velocity" for the file "/usr/wrk/people4/josc1234/nek5_visit/r095_Lx1_12_Ra1e8/vis.nek5000" could not be generated by the compute engine on host "localhost". >>>>>> >>>>>> >>>>>> >>>>>> My questions: >>>>>> >>>>>> Could it be that the graphics output should be in single precision? >>>>>> I saw that the people at KTH did have similar trouble. >>>>>> If yes, how can I switch to single precision in the usr file output? >>>>>> For smaller grid it worked. >>>>>> >>>>>> Thanks in advance, Joerg. >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>> _______________________________________________ >>> 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 Wed Mar 20 12:08:32 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 20 Mar 2013 18:08:32 +0100 Subject: [Nek5000-users] trouble with visit In-Reply-To: References: Message-ID: Dear all, Indeed, we believe that there are still some issues with Visit and 8-byte Nek5000 files, even in the latest Visit version 2.6.1. I attach below the previous communication we had on that. In short, Visit loads double-precision files, and some operations work without problems (3D contours), whereas other give wrong results (2D slices etc.). Best regards, Philipp and Reza. ________________________________________ From: Reza Dadfar [mailto:dadfar at kth.se] Sent: den 6 mars 2013 11:10 To: nek5000-users at lists.mcs.anl.gov Cc: pschlatt at mech.kth.se Subject: RE: [Nek5000-users] Visit reader for double precision f files Dear Neks, Reference to our previous question regarding reading double precision Nekton output file in Visit, we have tried to use the latest version of Visit, 2.6.1 However the problem is still there and visit cannot read the double precision Nekton files correctly. I was wondering if you could help us to solve this problem. With many thanks Reza ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Friday, November 16, 2012 4:04 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Visit reader for double precision f files Dear Neks, Reference to previous discussion (Sep.13th) about the support for the reading 64 bit files of nek5000 in VisIt, we have put up together a 3D cylinder as test case. For a double-precision format nek5000 dump file the 3D view and especially iso-contours are working fine whereas any 2D projection slice, or cut of the data is not working properly. In general operations considering the whole grid seem to work fine, but those related to a section of the grid such as box don't. This anomaly is happening regardless of choosing various pressure solver scheme (Pn_Pn/Pn_Pn-2) or including the grid data to be dumped in the file or not. I was wondering if you can help me with this issue. With many thanks Reza P.S. The 3D cylinder test-case located at the origin (0,0,0) of the coordinate system and extruded along the z-axis (perpendicular to the xy plane). The box extends from -15 to 25 in x direction, -9 to 9 in y direction and -2 to 2 in z directions. The mesh is constructed from the 2D cylinder in nek5000 repository. The number of elements is reduced, then extended in the z direction. An example of the dumped file can be found in the ftn: ftp://ftp.mech.kth.se/pub/pschlatt/nek5000 From nek5000-users at lists.mcs.anl.gov Mon Mar 25 16:46:18 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 25 Mar 2013 16:46:18 -0500 Subject: [Nek5000-users] Download and running of nek5000 Message-ID: Dear sir , I am a new mac user . I am trying to download the Nek5000 software but my MacBook Pro is telling me "Checked out revision 906 " . Later when I try to implement the different commands needed for the initial build I have lots of comment like "command not found" or " *** No rule to make target " and so on . This is what I have from my terminal : "Last login: Mon Mar 25 12:47:38 on ttys000 dhcp168:~ giacintogenco$ sudo svn co https://svn.mcs.anl.gov/repos/nek5/ svn: OPTIONS of 'https://svn.mcs.anl.gov/repos/nek5': Could not resolve hostname `svn.mcs.anl.gov': Host not found (https://svn.mcs.anl.gov) dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/maketools clean make: *** No rule to make target `clean'. Stop. dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/maketools all make: *** No targets specified and no makefile found. Stop. dhcp168:~ giacintogenco$ make -f -bash: syntax error near unexpected token `newline' dhcp168:~ giacintogenco$ svn co https://svn.mcs.anl.gov/repos/nek5/ nek5_svn Checked out revision 906. dhcp168:~ giacintogenco$ ~/nek_svn/trunk/tools/maketools -bash: /Users/giacintogenco/nek_svn/trunk/tools/maketools: No such file or directory dhcp168:~ giacintogenco$ sudo svn co https://svn.mcs.anl.gov/repos/nek5/ Password: Sorry, try again. Password: Checked out revision 906. dhcp168:~ giacintogenco$ nek5_svn/trunk/tools/maketools Usage: maketools [clean|all|tool(s)] dhcp168:~ giacintogenco$ nek5_svn/trunk/postnek/makefile -bash: nek5_svn/trunk/postnek/makefile: No such file or directory dhcp168:~ giacintogenco$ svn co https://svn.mcs.anl.gov/repos/nek5/ nek5_svn Checked out revision 906. dhcp168:~ giacintogenco$ nek5_svn/trunk/postnek/makefile -bash: nek5_svn/trunk/postnek/makefile: No such file or directory dhcp168:~ giacintogenco$ nek5_svn/trunk/tools/maketools Usage: maketools [clean|all|tool(s)] dhcp168:~ giacintogenco$ maketools all -bash: maketools: command not found dhcp168:~ giacintogenco$ maketools clean -bash: maketools: command not found dhcp168:~ giacintogenco$ ~nek5_svn/trunk/nek/makenek -bash: ~nek5_svn/trunk/nek/makenek: No such file or directory dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/nek/makenek makenek - automatic build tool for Nek5000 usage: makenek [.usr filename | clean] < -nocompile > dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/maketools clean make: *** No rule to make target `clean'. Stop. dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/maketools all make: *** No targets specified and no makefile found. Stop. dhcp168:~ giacintogenco$ " What do you suggest me to do ? It seems that I have all the files I need ( X11 , Mac OS X Lion , etc ) but they are "disconnected " . Please if you have a number of instructions I should follow please send me . I will follow all th hints and the instructions you suggest me to do to run the NEK5000 . Thank you ! Best Regards Giacinto Genco From nek5000-users at lists.mcs.anl.gov Tue Mar 26 08:43:57 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 26 Mar 2013 08:43:57 -0500 (CDT) Subject: [Nek5000-users] Download and running of nek5000 In-Reply-To: References: Message-ID: Dear Giacinto, The maketools command should be issued from ~/nek5_svn/trunk/tools where you would type: ./maketools (since it appears that "." is not in your path) Similarly, makenek should be issued from (say) one of the examples directories. It is normal to copy the makenek script to the location where you will build and run the example, so that makenek and SIZE are in the same directory, along with the .usr, .rea files, etc. I hope this helps. Paul Fischer On Mon, 25 Mar 2013, nek5000-users at lists.mcs.anl.gov wrote: > Dear sir , > I am a new mac user . I am trying to download the Nek5000 software but my MacBook Pro is telling me "Checked out revision 906 " . Later when I try to implement the different commands needed for the initial build I have lots of comment like "command not found" or " *** No rule to make target " and so on . > > This is what I have from my terminal : > > "Last login: Mon Mar 25 12:47:38 on ttys000 > dhcp168:~ giacintogenco$ sudo svn co https://svn.mcs.anl.gov/repos/nek5/ > svn: OPTIONS of 'https://svn.mcs.anl.gov/repos/nek5': Could not resolve hostname `svn.mcs.anl.gov': Host not found (https://svn.mcs.anl.gov) > dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/maketools clean > make: *** No rule to make target `clean'. Stop. > dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/maketools all > make: *** No targets specified and no makefile found. Stop. > dhcp168:~ giacintogenco$ make -f > -bash: syntax error near unexpected token `newline' > dhcp168:~ giacintogenco$ svn co https://svn.mcs.anl.gov/repos/nek5/ nek5_svn > Checked out revision 906. > dhcp168:~ giacintogenco$ ~/nek_svn/trunk/tools/maketools > -bash: /Users/giacintogenco/nek_svn/trunk/tools/maketools: No such file or directory > dhcp168:~ giacintogenco$ sudo svn co https://svn.mcs.anl.gov/repos/nek5/ > Password: > Sorry, try again. > Password: > Checked out revision 906. > dhcp168:~ giacintogenco$ nek5_svn/trunk/tools/maketools > Usage: maketools [clean|all|tool(s)] > dhcp168:~ giacintogenco$ nek5_svn/trunk/postnek/makefile > -bash: nek5_svn/trunk/postnek/makefile: No such file or directory > dhcp168:~ giacintogenco$ svn co https://svn.mcs.anl.gov/repos/nek5/ nek5_svn > Checked out revision 906. > dhcp168:~ giacintogenco$ nek5_svn/trunk/postnek/makefile > -bash: nek5_svn/trunk/postnek/makefile: No such file or directory > dhcp168:~ giacintogenco$ nek5_svn/trunk/tools/maketools > Usage: maketools [clean|all|tool(s)] > dhcp168:~ giacintogenco$ maketools all > -bash: maketools: command not found > dhcp168:~ giacintogenco$ maketools clean > -bash: maketools: command not found > dhcp168:~ giacintogenco$ ~nek5_svn/trunk/nek/makenek > -bash: ~nek5_svn/trunk/nek/makenek: No such file or directory > dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/nek/makenek > makenek - automatic build tool for Nek5000 > > usage: makenek [.usr filename | clean] < -nocompile > > > dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/maketools clean > make: *** No rule to make target `clean'. Stop. > dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/maketools all > make: *** No targets specified and no makefile found. Stop. > dhcp168:~ giacintogenco$ " > > What do you suggest me to do ? It seems that I have all the files I need ( X11 , Mac OS X Lion , etc ) but they are "disconnected " . Please if you have a number of instructions I should follow please send me . I will follow all th hints and the instructions you suggest me to do to run the NEK5000 . > > Thank you ! > > Best Regards > > Giacinto Genco > _______________________________________________ > 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 Mar 26 10:02:26 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 26 Mar 2013 10:02:26 -0500 Subject: [Nek5000-users] Download and running of nek5000 In-Reply-To: References: Message-ID: Dear Paul , thanks for your kind reply and useful information . The terminal says : "Giacinto-Gencos-MacBook-Pro:~ giacintogenco$ ~/nek5_svn/trunk/tools -bash: /Users/giacintogenco/nek5_svn/trunk/tools: is a directory Giacinto-Gencos-MacBook-Pro:~ giacintogenco$ ./maketools -bash: ./maketools: No such file or directory Giacinto-Gencos-MacBook-Pro:~ giacintogenco$ " How can I create the directory ? Maybe it is easier than I think , but I am stuck here . Thank you for your precious help , Best Regards Giacinto Genco On Tue, Mar 26, 2013 at 8:43 AM, wrote: > > Dear Giacinto, > > The maketools command should be issued from > > ~/nek5_svn/trunk/tools > > where you would type: > > ./maketools (since it appears that "." is not in your path) > > Similarly, makenek should be issued from (say) one of the > examples directories. It is normal to copy the makenek > script to the location where you will build and run the > example, so that makenek and SIZE are in the same directory, > along with the .usr, .rea files, etc. > > I hope this helps. > > Paul Fischer > > > > On Mon, 25 Mar 2013, nek5000-users at lists.mcs.anl.**govwrote: > > Dear sir , >> I am a new mac user . I am trying to download the Nek5000 software but my >> MacBook Pro is telling me "Checked out revision 906 " . Later when I try to >> implement the different commands needed for the initial build I have lots >> of comment like "command not found" or " *** No rule to make target " and >> so on . >> >> This is what I have from my terminal : >> >> "Last login: Mon Mar 25 12:47:38 on ttys000 >> dhcp168:~ giacintogenco$ sudo svn co https://svn.mcs.anl.gov/repos/** >> nek5/ >> svn: OPTIONS of 'https://svn.mcs.anl.gov/**repos/nek5': >> Could not resolve hostname `svn.mcs.anl.gov': Host not found ( >> https://svn.mcs.anl.gov) >> dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/**maketools clean >> make: *** No rule to make target `clean'. Stop. >> dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/**maketools all >> make: *** No targets specified and no makefile found. Stop. >> dhcp168:~ giacintogenco$ make -f >> -bash: syntax error near unexpected token `newline' >> dhcp168:~ giacintogenco$ svn co https://svn.mcs.anl.gov/repos/**nek5/nek5_svn >> Checked out revision 906. >> dhcp168:~ giacintogenco$ ~/nek_svn/trunk/tools/**maketools >> -bash: /Users/giacintogenco/nek_svn/**trunk/tools/maketools: No such >> file or directory >> dhcp168:~ giacintogenco$ sudo svn co https://svn.mcs.anl.gov/repos/** >> nek5/ >> Password: >> Sorry, try again. >> Password: >> Checked out revision 906. >> dhcp168:~ giacintogenco$ nek5_svn/trunk/tools/maketools >> Usage: maketools [clean|all|tool(s)] >> dhcp168:~ giacintogenco$ nek5_svn/trunk/postnek/**makefile >> -bash: nek5_svn/trunk/postnek/**makefile: No such file or directory >> dhcp168:~ giacintogenco$ svn co https://svn.mcs.anl.gov/repos/**nek5/nek5_svn >> Checked out revision 906. >> dhcp168:~ giacintogenco$ nek5_svn/trunk/postnek/**makefile >> -bash: nek5_svn/trunk/postnek/**makefile: No such file or directory >> dhcp168:~ giacintogenco$ nek5_svn/trunk/tools/maketools >> Usage: maketools [clean|all|tool(s)] >> dhcp168:~ giacintogenco$ maketools all >> -bash: maketools: command not found >> dhcp168:~ giacintogenco$ maketools clean >> -bash: maketools: command not found >> dhcp168:~ giacintogenco$ ~nek5_svn/trunk/nek/makenek >> -bash: ~nek5_svn/trunk/nek/makenek: No such file or directory >> dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/nek/makenek >> makenek - automatic build tool for Nek5000 >> >> usage: makenek [.usr filename | clean] < -nocompile > >> >> dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/**maketools clean >> make: *** No rule to make target `clean'. Stop. >> dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/**maketools all >> make: *** No targets specified and no makefile found. Stop. >> dhcp168:~ giacintogenco$ " >> >> What do you suggest me to do ? It seems that I have all the files I need >> ( X11 , Mac OS X Lion , etc ) but they are "disconnected " . Please if you >> have a number of instructions I should follow please send me . I will >> follow all th hints and the instructions you suggest me to do to run the >> NEK5000 . >> >> Thank you ! >> >> Best Regards >> >> Giacinto Genco >> ______________________________**_________________ >> 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 > -- Giacinto M. F. Genco Master of Science in Nuclear Engineering , Purdue University Master of Science in Aerospace Engineering , Purdue University Italian " Laurea " in Mechanical Engineering , Politecnico di Bari , Bari , Italy . -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Mar 26 10:41:41 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 26 Mar 2013 10:41:41 -0500 (CDT) Subject: [Nek5000-users] Download and running of nek5000 In-Reply-To: Message-ID: Hi Giacinto, Google unix commands -- perhaps, the following will be helpful http://doors.stanford.edu/~sr/computing/basic-unix.html Also your can read the wiki to learn more about Nek http://nek5000.mcs.anl.gov/index.php/UG Best. Aleks ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Tuesday, March 26, 2013 10:02:26 AM Subject: Re: [Nek5000-users] Download and running of nek5000 Dear Paul , thanks for your kind reply and useful information . The terminal says : "Giacinto-Gencos-MacBook-Pro:~ giacintogenco$ ~/nek5_svn/trunk/tools -bash: /Users/giacintogenco/nek5_svn/trunk/tools: is a directory Giacinto-Gencos-MacBook-Pro:~ giacintogenco$ ./maketools -bash: ./maketools: No such file or directory Giacinto-Gencos-MacBook-Pro:~ giacintogenco$ " How can I create the directory ? Maybe it is easier than I think , but I am stuck here . Thank you for your precious help , Best Regards Giacinto Genco On Tue, Mar 26, 2013 at 8:43 AM, < nek5000-users at lists.mcs.anl.gov > wrote: Dear Giacinto, The maketools command should be issued from ~/nek5_svn/trunk/tools where you would type: ./maketools (since it appears that "." is not in your path) Similarly, makenek should be issued from (say) one of the examples directories. It is normal to copy the makenek script to the location where you will build and run the example, so that makenek and SIZE are in the same directory, along with the .usr, .rea files, etc. I hope this helps. Paul Fischer On Mon, 25 Mar 2013, nek5000-users at lists.mcs.anl. gov wrote: Dear sir , I am a new mac user . I am trying to download the Nek5000 software but my MacBook Pro is telling me "Checked out revision 906 " . Later when I try to implement the different commands needed for the initial build I have lots of comment like "command not found" or " *** No rule to make target " and so on . This is what I have from my terminal : "Last login: Mon Mar 25 12:47:38 on ttys000 dhcp168:~ giacintogenco$ sudo svn co https://svn.mcs.anl.gov/repos/ nek5/ svn: OPTIONS of ' https://svn.mcs.anl.gov/ repos/nek5 ': Could not resolve hostname ` svn.mcs.anl.gov ': Host not found ( https://svn.mcs.anl.gov ) dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/ maketools clean make: *** No rule to make target `clean'. Stop. dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/ maketools all make: *** No targets specified and no makefile found. Stop. dhcp168:~ giacintogenco$ make -f -bash: syntax error near unexpected token `newline' dhcp168:~ giacintogenco$ svn co https://svn.mcs.anl.gov/repos/ nek5/ nek5_svn Checked out revision 906. dhcp168:~ giacintogenco$ ~/nek_svn/trunk/tools/ maketools -bash: /Users/giacintogenco/nek_svn/ trunk/tools/maketools: No such file or directory dhcp168:~ giacintogenco$ sudo svn co https://svn.mcs.anl.gov/repos/ nek5/ Password: Sorry, try again. Password: Checked out revision 906. dhcp168:~ giacintogenco$ nek5_svn/trunk/tools/maketools Usage: maketools [clean|all|tool(s)] dhcp168:~ giacintogenco$ nek5_svn/trunk/postnek/ makefile -bash: nek5_svn/trunk/postnek/ makefile: No such file or directory dhcp168:~ giacintogenco$ svn co https://svn.mcs.anl.gov/repos/ nek5/ nek5_svn Checked out revision 906. dhcp168:~ giacintogenco$ nek5_svn/trunk/postnek/ makefile -bash: nek5_svn/trunk/postnek/ makefile: No such file or directory dhcp168:~ giacintogenco$ nek5_svn/trunk/tools/maketools Usage: maketools [clean|all|tool(s)] dhcp168:~ giacintogenco$ maketools all -bash: maketools: command not found dhcp168:~ giacintogenco$ maketools clean -bash: maketools: command not found dhcp168:~ giacintogenco$ ~nek5_svn/trunk/nek/makenek -bash: ~nek5_svn/trunk/nek/makenek: No such file or directory dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/nek/makenek makenek - automatic build tool for Nek5000 usage: makenek [.usr filename | clean] < -nocompile > dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/ maketools clean make: *** No rule to make target `clean'. Stop. dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/ maketools all make: *** No targets specified and no makefile found. Stop. dhcp168:~ giacintogenco$ " What do you suggest me to do ? It seems that I have all the files I need ( X11 , Mac OS X Lion , etc ) but they are "disconnected " . Please if you have a number of instructions I should follow please send me . I will follow all th hints and the instructions you suggest me to do to run the NEK5000 . Thank you ! Best Regards Giacinto Genco ______________________________ _________________ 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 -- Giacinto M. F. Genco Master of Science in Nuclear Engineering , Purdue University Master of Science in Aerospace Engineering , Purdue University Italian " Laurea " in Mechanical Engineering , Politecnico di Bari , Bari , Italy . _______________________________________________ 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 Mar 26 17:50:39 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 26 Mar 2013 17:50:39 -0500 Subject: [Nek5000-users] Download and running of nek5000 In-Reply-To: References: Message-ID: Hello Alex ! Thanks for the very useful links . I am a Ph.D student working for Professor A. Ostrogorsky at IIT in Chicago . I am trying to install Nek5000 on my Mac Personal computer , in order to run FE elements simulations on my mac pc . I partially solved my problem but now the terminal is saying : " Last login: Tue Mar 26 17:39:07 on ttys000 Giacinto-Gencos-MacBook-Pro:~ giacintogenco$ ~/bin/prex Can't open display Did you setenv DISPLAY to your localHost and xhost + on the local display? Giacinto-Gencos-MacBook-Pro:~ giacintogenco$ " Now I do not know how to solve this " display " , but hope and think is no big deal . Can you give me an advice on what to do ? Thank you very much indeed since now , Best Regards , sincerely Giacinto M. F. Genco On Tue, Mar 26, 2013 at 10:41 AM, wrote: > Hi Giacinto, > > Google unix commands -- perhaps, the following will be helpful > > http://doors.stanford.edu/~sr/computing/basic-unix.html > > > Also your can read the wiki to learn more about Nek > > http://nek5000.mcs.anl.gov/index.php/UG > > Best. > Aleks > > > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Sent: Tuesday, March 26, 2013 10:02:26 AM > Subject: Re: [Nek5000-users] Download and running of nek5000 > > > > Dear Paul , > thanks for your kind reply and useful information . The terminal says : > > > "Giacinto-Gencos-MacBook-Pro:~ giacintogenco$ ~/nek5_svn/trunk/tools > -bash: /Users/giacintogenco/nek5_svn/trunk/tools: is a directory > Giacinto-Gencos-MacBook-Pro:~ giacintogenco$ ./maketools > -bash: ./maketools: No such file or directory > Giacinto-Gencos-MacBook-Pro:~ giacintogenco$ " > > > How can I create the directory ? Maybe it is easier than I think , but I > am stuck here . Thank you for your precious help , > > > Best Regards > > > Giacinto Genco > > > > > > > > On Tue, Mar 26, 2013 at 8:43 AM, < nek5000-users at lists.mcs.anl.gov > > wrote: > > > > Dear Giacinto, > > The maketools command should be issued from > > ~/nek5_svn/trunk/tools > > where you would type: > > ./maketools (since it appears that "." is not in your path) > > Similarly, makenek should be issued from (say) one of the > examples directories. It is normal to copy the makenek > script to the location where you will build and run the > example, so that makenek and SIZE are in the same directory, > along with the .usr, .rea files, etc. > > I hope this helps. > > Paul Fischer > > > > > On Mon, 25 Mar 2013, nek5000-users at lists.mcs.anl. gov wrote: > > > > Dear sir , > I am a new mac user . I am trying to download the Nek5000 software but my > MacBook Pro is telling me "Checked out revision 906 " . Later when I try to > implement the different commands needed for the initial build I have lots > of comment like "command not found" or " *** No rule to make target " and > so on . > > This is what I have from my terminal : > > "Last login: Mon Mar 25 12:47:38 on ttys000 > dhcp168:~ giacintogenco$ sudo svn co https://svn.mcs.anl.gov/repos/ nek5/ > svn: OPTIONS of ' https://svn.mcs.anl.gov/ repos/nek5 ': Could not > resolve hostname ` svn.mcs.anl.gov ': Host not found ( > https://svn.mcs.anl.gov ) > dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/ maketools clean > make: *** No rule to make target `clean'. Stop. > dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/ maketools all > make: *** No targets specified and no makefile found. Stop. > dhcp168:~ giacintogenco$ make -f > -bash: syntax error near unexpected token `newline' > dhcp168:~ giacintogenco$ svn co https://svn.mcs.anl.gov/repos/ nek5/ > nek5_svn > Checked out revision 906. > dhcp168:~ giacintogenco$ ~/nek_svn/trunk/tools/ maketools > -bash: /Users/giacintogenco/nek_svn/ trunk/tools/maketools: No such file > or directory > dhcp168:~ giacintogenco$ sudo svn co https://svn.mcs.anl.gov/repos/ nek5/ > Password: > Sorry, try again. > Password: > Checked out revision 906. > dhcp168:~ giacintogenco$ nek5_svn/trunk/tools/maketools > Usage: maketools [clean|all|tool(s)] > dhcp168:~ giacintogenco$ nek5_svn/trunk/postnek/ makefile > -bash: nek5_svn/trunk/postnek/ makefile: No such file or directory > dhcp168:~ giacintogenco$ svn co https://svn.mcs.anl.gov/repos/ nek5/ > nek5_svn > Checked out revision 906. > dhcp168:~ giacintogenco$ nek5_svn/trunk/postnek/ makefile > -bash: nek5_svn/trunk/postnek/ makefile: No such file or directory > dhcp168:~ giacintogenco$ nek5_svn/trunk/tools/maketools > Usage: maketools [clean|all|tool(s)] > dhcp168:~ giacintogenco$ maketools all > -bash: maketools: command not found > dhcp168:~ giacintogenco$ maketools clean > -bash: maketools: command not found > dhcp168:~ giacintogenco$ ~nek5_svn/trunk/nek/makenek > -bash: ~nek5_svn/trunk/nek/makenek: No such file or directory > dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/nek/makenek > makenek - automatic build tool for Nek5000 > > usage: makenek [.usr filename | clean] < -nocompile > > > dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/ maketools clean > make: *** No rule to make target `clean'. Stop. > dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/ maketools all > make: *** No targets specified and no makefile found. Stop. > dhcp168:~ giacintogenco$ " > > What do you suggest me to do ? It seems that I have all the files I need ( > X11 , Mac OS X Lion , etc ) but they are "disconnected " . Please if you > have a number of instructions I should follow please send me . I will > follow all th hints and the instructions you suggest me to do to run the > NEK5000 . > > Thank you ! > > Best Regards > > Giacinto Genco > ______________________________ _________________ > 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 > > > > > -- > Giacinto M. F. Genco > Master of Science in Nuclear Engineering , Purdue University > Master of Science in Aerospace Engineering , Purdue University > Italian " Laurea " in Mechanical Engineering , Politecnico di Bari , Bari > , Italy . > > _______________________________________________ > 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 > -- Giacinto M. F. Genco Master of Science in Nuclear Engineering , Purdue University Master of Science in Aerospace Engineering , Purdue University Italian " Laurea " in Mechanical Engineering , Politecnico di Bari , Bari , Italy . -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 27 07:00:28 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 27 Mar 2013 07:00:28 -0500 (CDT) Subject: [Nek5000-users] Download and running of nek5000 In-Reply-To: Message-ID: Hi Giacinto, Please, contact me offline at obabko at mcs.anl.gov Best. Aleks ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Tuesday, March 26, 2013 5:50:39 PM Subject: Re: [Nek5000-users] Download and running of nek5000 Hello Alex ! Thanks for the very useful links . I am a Ph.D student working for Professor A. Ostrogorsky at IIT in Chicago . I am trying to install Nek5000 on my Mac Personal computer , in order to run FE elements simulations on my mac pc . I partially solved my problem but now the terminal is saying : " Last login: Tue Mar 26 17:39:07 on ttys000 Giacinto-Gencos-MacBook-Pro:~ giacintogenco$ ~/bin/prex Can't open display Did you setenv DISPLAY to your localHost and xhost + on the local display? Giacinto-Gencos-MacBook-Pro:~ giacintogenco$ " Now I do not know how to solve this " display " , but hope and think is no big deal . Can you give me an advice on what to do ? Thank you very much indeed since now , Best Regards , sincerely Giacinto M. F. Genco On Tue, Mar 26, 2013 at 10:41 AM, < nek5000-users at lists.mcs.anl.gov > wrote: Hi Giacinto, Google unix commands -- perhaps, the following will be helpful http://doors.stanford.edu/~sr/computing/basic-unix.html Also your can read the wiki to learn more about Nek http://nek5000.mcs.anl.gov/index.php/UG Best. Aleks ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Tuesday, March 26, 2013 10:02:26 AM Subject: Re: [Nek5000-users] Download and running of nek5000 Dear Paul , thanks for your kind reply and useful information . The terminal says : "Giacinto-Gencos-MacBook-Pro:~ giacintogenco$ ~/nek5_svn/trunk/tools -bash: /Users/giacintogenco/nek5_svn/trunk/tools: is a directory Giacinto-Gencos-MacBook-Pro:~ giacintogenco$ ./maketools -bash: ./maketools: No such file or directory Giacinto-Gencos-MacBook-Pro:~ giacintogenco$ " How can I create the directory ? Maybe it is easier than I think , but I am stuck here . Thank you for your precious help , Best Regards Giacinto Genco On Tue, Mar 26, 2013 at 8:43 AM, < nek5000-users at lists.mcs.anl.gov > wrote: Dear Giacinto, The maketools command should be issued from ~/nek5_svn/trunk/tools where you would type: ./maketools (since it appears that "." is not in your path) Similarly, makenek should be issued from (say) one of the examples directories. It is normal to copy the makenek script to the location where you will build and run the example, so that makenek and SIZE are in the same directory, along with the .usr, .rea files, etc. I hope this helps. Paul Fischer On Mon, 25 Mar 2013, nek5000-users at lists.mcs.anl. gov wrote: Dear sir , I am a new mac user . I am trying to download the Nek5000 software but my MacBook Pro is telling me "Checked out revision 906 " . Later when I try to implement the different commands needed for the initial build I have lots of comment like "command not found" or " *** No rule to make target " and so on . This is what I have from my terminal : "Last login: Mon Mar 25 12:47:38 on ttys000 dhcp168:~ giacintogenco$ sudo svn co https://svn.mcs.anl.gov/repos/ nek5/ svn: OPTIONS of ' https://svn.mcs.anl.gov/ repos/nek5 ': Could not resolve hostname ` svn.mcs.anl.gov ': Host not found ( https://svn.mcs.anl.gov ) dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/ maketools clean make: *** No rule to make target `clean'. Stop. dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/ maketools all make: *** No targets specified and no makefile found. Stop. dhcp168:~ giacintogenco$ make -f -bash: syntax error near unexpected token `newline' dhcp168:~ giacintogenco$ svn co https://svn.mcs.anl.gov/repos/ nek5/ nek5_svn Checked out revision 906. dhcp168:~ giacintogenco$ ~/nek_svn/trunk/tools/ maketools -bash: /Users/giacintogenco/nek_svn/ trunk/tools/maketools: No such file or directory dhcp168:~ giacintogenco$ sudo svn co https://svn.mcs.anl.gov/repos/ nek5/ Password: Sorry, try again. Password: Checked out revision 906. dhcp168:~ giacintogenco$ nek5_svn/trunk/tools/maketools Usage: maketools [clean|all|tool(s)] dhcp168:~ giacintogenco$ nek5_svn/trunk/postnek/ makefile -bash: nek5_svn/trunk/postnek/ makefile: No such file or directory dhcp168:~ giacintogenco$ svn co https://svn.mcs.anl.gov/repos/ nek5/ nek5_svn Checked out revision 906. dhcp168:~ giacintogenco$ nek5_svn/trunk/postnek/ makefile -bash: nek5_svn/trunk/postnek/ makefile: No such file or directory dhcp168:~ giacintogenco$ nek5_svn/trunk/tools/maketools Usage: maketools [clean|all|tool(s)] dhcp168:~ giacintogenco$ maketools all -bash: maketools: command not found dhcp168:~ giacintogenco$ maketools clean -bash: maketools: command not found dhcp168:~ giacintogenco$ ~nek5_svn/trunk/nek/makenek -bash: ~nek5_svn/trunk/nek/makenek: No such file or directory dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/nek/makenek makenek - automatic build tool for Nek5000 usage: makenek [.usr filename | clean] < -nocompile > dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/ maketools clean make: *** No rule to make target `clean'. Stop. dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/ maketools all make: *** No targets specified and no makefile found. Stop. dhcp168:~ giacintogenco$ " What do you suggest me to do ? It seems that I have all the files I need ( X11 , Mac OS X Lion , etc ) but they are "disconnected " . Please if you have a number of instructions I should follow please send me . I will follow all th hints and the instructions you suggest me to do to run the NEK5000 . Thank you ! Best Regards Giacinto Genco ______________________________ _________________ 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 -- Giacinto M. F. Genco Master of Science in Nuclear Engineering , Purdue University Master of Science in Aerospace Engineering , Purdue University Italian " Laurea " in Mechanical Engineering , Politecnico di Bari , Bari , Italy . _______________________________________________ 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 -- Giacinto M. F. Genco Master of Science in Nuclear Engineering , Purdue University Master of Science in Aerospace Engineering , Purdue University Italian " Laurea " in Mechanical Engineering , Politecnico di Bari , Bari , Italy . _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users