tag:blogger.com,1999:blog-5188121942175615593.post8904835285966324308..comments2024-03-29T01:51:12.527+11:00Comments on Lindqvist -- a blog about Linux and Science. Mostly.: 268. Compiling and testing GAMESS US on debian testing (wheezy)lindqvisthttp://www.blogger.com/profile/11525548328692436184noreply@blogger.comBlogger17125tag:blogger.com,1999:blog-5188121942175615593.post-63585768470783195532020-04-06T20:03:59.804+10:002020-04-06T20:03:59.804+10:00Hello! I am a mac user. And now im trying to insta...Hello! I am a mac user. And now im trying to install the latest version of GAMESS on mac. But i have a problem: it doesnt recognise the 9.3 version of gfortran. What can i do? and how can i know which version is the last to recognise?Gregoryhttps://www.blogger.com/profile/13867616084067764858noreply@blogger.comtag:blogger.com,1999:blog-5188121942175615593.post-80772202490619703202013-05-12T22:11:46.576+10:002013-05-12T22:11:46.576+10:00I've since compiled gamess with GPU support an...I've since compiled gamess with GPU support and I think I have a better understanding of what Кирилл Березовский was trying to tell me. Like him, I built according to the instructions in aaa.readme.1st, and like him, while everything is working fine, the GPU is not being used. <br /><br />Hence, ignore my replies above, and have a look here instead:<br />http://verahill.blogspot.com.au/2013/05/409-failed-attempt-at-compiling-gamess_10.html<br />http://verahill.blogspot.com.au/2013/05/409a-failed-attempt-at-compiling-gamess.html<br />lindqvisthttps://www.blogger.com/profile/11525548328692436184noreply@blogger.comtag:blogger.com,1999:blog-5188121942175615593.post-74684577403758801682013-03-13T10:10:07.611+11:002013-03-13T10:10:07.611+11:00Kirill,
I shouldn't pretend to know things I d...Kirill,<br />I shouldn't pretend to know things I don't. From what (little) I understand though MPI can spawn threads on CPU cores, but not GPU. Also, you don't manage the GPU cores individually, but as a device. Again, it's all very fuzzy in my head, and I have no expertise in this.<br /><br />See e.g. http://stackoverflow.com/questions/10237443/mpi-vs-gpu-vs-hadoop-what-are-the-major-difference-between-these-three-parallel<br />"[..] MPI and CUDA are completely orthogonal to each other."<br /><br />The only GPU calcs I've done are described here:<br />http://verahill.blogspot.com.au/search?q=gromacs+gpu<br /><br />Finally, you probably can't expect all types of calculations to be able to take advantage of the GPU e.g. gamess might only use it for implicit solvation (PCM, COSMO), but do most of the heavy lifting on the CPU. Again, I'm just speculating.<br /><br />That's certainly true for Firefly (says it doesn't use it for DFT)lindqvisthttps://www.blogger.com/profile/11525548328692436184noreply@blogger.comtag:blogger.com,1999:blog-5188121942175615593.post-11861410451522859952013-03-13T02:56:03.767+11:002013-03-13T02:56:03.767+11:00Dear lindqvist,
First of all I want to thank you ...Dear lindqvist,<br /><br />First of all I want to thank you very much for your replies!<br /><br />Yes, I saw Firefly before GAMESS. In past there was problem with registration on Firefly_forum, and I left that idea, but now it's become good! Thank you!<br /><br />Other side, tonight I noticed special GAMESS version - special for NVIDIA GPU's. It was released recently, as Andrey Asadchev (author) say to me month ago! There are new scripts and new documentation inside, so I will work hard right now!<br /><br />Still, I have some points to answer to you.<br /><br />* Yes, I was linked GAMESS+CUDA using manual above. But also I'm using official GAMESS manual (in .../gamess/libcchem/aaa.readme.1st). <br /><br />* I compiled successfully CPU-version (sockets, mpi - doesn't matter, everything works) and GPU-version. Well, both calculates... but in second version GPU still passive! I cannot understand why. Maybe there's incorrect input file?..<br /><br />* In your opinion, why I shouldn't using MPI? GPU-block places in MPI-block in script 'rungms'..Anonymoushttps://www.blogger.com/profile/01688441971853180344noreply@blogger.comtag:blogger.com,1999:blog-5188121942175615593.post-85770815756292696122013-03-12T12:52:06.140+11:002013-03-12T12:52:06.140+11:00Another idea: Firefly (i.e. former PC Gamess) may ...Another idea: Firefly (i.e. former PC Gamess) may or may not support CUDA/GPU. It's not completely clear from the site:<br />http://classic.chem.msu.su/gran/gamess/index.html<br />http://classic.chem.msu.su/gran/gamess/cuding.html<br />http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/?C35e9ea902bHW-8412-1040+00.htm<br />http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/?C35e9ea902bHW-8385-830+00.htmlindqvisthttps://www.blogger.com/profile/11525548328692436184noreply@blogger.comtag:blogger.com,1999:blog-5188121942175615593.post-75005826450155539172013-03-12T12:36:22.972+11:002013-03-12T12:36:22.972+11:00I just noticed that you had posted a comment on th...I just noticed that you had posted a comment on that page.<br /><br />I don't think you can use mpi and CUDA/GPU.<br /><br />That also means that you shouldn't use mpiexec to run.<br /><br />Did you obtain a gamess.gpu.x binary? If you do ldd on it, is it properly linked to the CUDA libs?<br /><br />Beyond that, I actually don't know what the best way forward is. I'll post something here if I come across anything.lindqvisthttps://www.blogger.com/profile/11525548328692436184noreply@blogger.comtag:blogger.com,1999:blog-5188121942175615593.post-80889779093890077612013-03-12T12:24:17.533+11:002013-03-12T12:24:17.533+11:00What guide did you follow when you built your GPU-...What guide did you follow when you built your GPU-enabled version?<br /><br />This one? http://combichem.blogspot.com.au/2011/02/compiling-gamess-with-cuda-gpu-support.htmllindqvisthttps://www.blogger.com/profile/11525548328692436184noreply@blogger.comtag:blogger.com,1999:blog-5188121942175615593.post-35102011067609283982013-03-12T09:36:47.015+11:002013-03-12T09:36:47.015+11:00Dear lindqvist,
Unfortunatelly there's a probl...Dear lindqvist,<br />Unfortunatelly there's a problem. Compilation successful, but GPU doesn't works, only CPU calculations! I tried to understand my problem, looked hard to run-scripts, but no idea, what's wrong. I wrote a message to you and to GAMESS_forum. Well... hope I'll find the answer... because I'm a student, I'll graduate soon, and I really don't what to do -- this is my diploma, main thing of my research (theme: GPU calculations).Anonymoushttps://www.blogger.com/profile/01688441971853180344noreply@blogger.comtag:blogger.com,1999:blog-5188121942175615593.post-33282275265670976232013-03-11T10:38:18.312+11:002013-03-11T10:38:18.312+11:00Kirill,
I don't have any experience of using G...Kirill,<br />I don't have any experience of using GAMESS(US) with CUDA support since I lack suitable (i.e. dynamically cooled) hardware -- also, I have to admit that I haven't been using gamess much since nwchem has served me well (wish it had a wider range of solvent models though). Have you managed to compile GAMESS with GPU support?lindqvisthttps://www.blogger.com/profile/11525548328692436184noreply@blogger.comtag:blogger.com,1999:blog-5188121942175615593.post-38187098545782857132013-03-11T09:40:30.631+11:002013-03-11T09:40:30.631+11:00Dear lindqvist,
Do you have experience in running...Dear lindqvist,<br /><br />Do you have experience in running GAMESS (US) with GPU (NVIDIA CUDA)?<br /><br />Best regards, Kirill.Anonymoushttps://www.blogger.com/profile/01688441971853180344noreply@blogger.comtag:blogger.com,1999:blog-5188121942175615593.post-49806020756511866462012-10-28T09:21:10.214+11:002012-10-28T09:21:10.214+11:00Pietro,
it's the optimisation. I set the opti...Pietro, <br />it's the optimisation. I set the optimisation to -O0 in ddi/compddi (lines 433, 699, 707), comp (line 1664) and lked (line 487).<br /><br />This time exam44.inp runs perfectly.lindqvisthttps://www.blogger.com/profile/11525548328692436184noreply@blogger.comtag:blogger.com,1999:blog-5188121942175615593.post-63997449804183085852012-10-27T18:04:23.149+11:002012-10-27T18:04:23.149+11:00Pietro,
I think it might be wise to contact Mike S...Pietro,<br />I think it might be wise to contact Mike Schmidt (http://www.msg.chem.iastate.edu/~mike/) or possibly first post a general enquiry at the independent gamess list at http://groups.google.com/group/gamess<br /><br />You have a compelling set of data for what seems to be a bug, or at least unintended behaviour.<br /><br />I'm not an expert, so don't know if the answer is here: http://gcc.gnu.org/gcc-4.7/changes.html<br /><br />I will recompile gamess in a few days without any optimisation (-O0) and see if the problem persists. Something I read somewhere got me thinking...<br /><br />I'll post the outcome here.lindqvisthttps://www.blogger.com/profile/11525548328692436184noreply@blogger.comtag:blogger.com,1999:blog-5188121942175615593.post-66685812680128275382012-10-27T11:28:01.978+11:002012-10-27T11:28:01.978+11:00Hi,
I confirmed that it's a gcc/gfortran 4.7 i...Hi,<br />I confirmed that it's a gcc/gfortran 4.7 issue. In particular I compiled GAMESS with:<br />1) on a Fedora 17 box with gcc/gfortran 4.7 + ATLAS (rebuilt with gcc 4.7 and repackaged to optimize them on the same box used for calculations. Incidentally, 4.7 required a patch to compile...);<br />2) same box and compilers as 1) + OpenBLAS built on the same box with 4.7 compilers;<br />3) same box as 1-2), gcc/gfortran 4.6 + same ATLAS as 1;<br />4) same box as 1-3), gcc/gfortran 4.6 + OpenBLAS built on the same box with 4.6 compilers;<br />5) a different Fedora 16 box, gcc/gfortran 4.6 + standard ATLAS;<br />6) same box and compilers as 5) + OpenBLAS built on the same box with 4.6 compilers.<br /><br />The strange oscillating behaviour was observed for exam44 when running 1) and 2) executables only, the other combinations were all OK.<br /><br />I also made some tests on a real input (a 6-31G* HF geometry optimization) to evaluate performances of all the above versions and the overall behaviour of 1-2). These latter provided reasonable results, almost identical to those obtained with all other executables.<br />Performances were quite similar between ATLAS and OpenBLAS on both the architectures I tested (double Xeon boxes with either Core2 or Nehalem processors), but I sadly still have no Sandy Bridge CPU handy...<br /><br />An additional note: I had to compile the single-threaded version of OpenBLAS to prevent runtime issues when using > 1/2 of the available cores and performance issues in all cases (maybe advantages can be obtained when running calculation types making a heavier usage of OpenBLAS routines than the simple HF geometry optimization I used to compare performances).<br /><br />Best,<br />PietroAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-5188121942175615593.post-52913351432572216432012-10-26T05:27:21.232+11:002012-10-26T05:27:21.232+11:00Perfect. I like you blog and I add it to my favori...Perfect. I like you blog and I add it to my favorite.<br />Shahabnoreply@blogger.comtag:blogger.com,1999:blog-5188121942175615593.post-79677255783257750982012-10-19T20:30:42.599+11:002012-10-19T20:30:42.599+11:00And now I've tried it using a version compiled...And now I've tried it using a version compiled with gcc 4.1.2 -- it converges:<br />1 -598.7948005066<br />2 -599.9236549126<br />3 -599.9656190200<br />4 -599.9683370713<br />5 -599.9687731854<br />6 -599.9687786560<br />7 -599.9687798305<br />8 -599.9687803241<br />9 -599.9687803808<br />10 -599.9687803950<br />11 -599.9687803940<br />12 -599.9687803934lindqvisthttps://www.blogger.com/profile/11525548328692436184noreply@blogger.comtag:blogger.com,1999:blog-5188121942175615593.post-67468342511629082532012-10-19T20:23:29.190+11:002012-10-19T20:23:29.190+11:00I tried running test 44, and I observe the same th...I tried running test 44, and I observe the same thing as you did in that the energy oscillates and doesn't converge:<br />1 -598.7948005066<br />2 144.4750515060<br />3 140.1905075316<br />4 140.1538501955<br />5 140.1904325458<br />6 51.1643688518<br />7 140.1477528877<br />8 140.1904315544<br />9 140.1538500948<br />10 51.1643688561<br />11 140.1477528877<br />12 140.1904315544<br />13 140.1538500948<br />14 51.1643688561<br />15 140.1477528877<br />16 140.1904315544<br />17 140.1538500947<br />18 51.1643688561<br />19 140.1477528877<br />20 140.1904315544<br />21 140.1538500947<br />22 51.1643688561<br />23 140.1477528877<br />24 140.1904315544<br />25 140.1538500947<br />26 51.1643688561<br />27 140.1477528877<br />28 140.1904315544<br />29 140.1538500947<br />lindqvisthttps://www.blogger.com/profile/11525548328692436184noreply@blogger.comtag:blogger.com,1999:blog-5188121942175615593.post-51577700825775101342012-10-19T14:26:48.764+11:002012-10-19T14:26:48.764+11:00Hi,
have you run GAMESS tests after compiling wit...Hi,<br /><br />have you run GAMESS tests after compiling with gfortran 4.7? I compiled using both (a home repackaged version, with x86_64 ss3 optimization, of) atlas, and with OpenBLAS on a Fedora Core 17 machine featuring gcc 4.7 compilers and in both cases I obtained a strange result: 46 of 47 tests were passed but exam44, which doesn't converge, since SCF exhibits an oscillatory behaviour. Searching the web somebody else apparently got the same issue, although the page I found only reported the output of the test summary.<br />The same 12r1 version, compiled on a FC16 box with gcc 4.6 and standard atlas, passed all tests.<br />Later I'm going to perform other experiments by mixing gcc versions,math libraries and machines. If you are interested, I'll send a more complete report of my tests.<br /><br />Best,<br />Pietro Amodeo, ICB-CNR Pozzuoli (NA( - ItalyAnonymousnoreply@blogger.com