Justin, Sorry for not giving the correct information.
Gromacs version 4.5.5 Tesla card- Nvidia Tesla S1070 (Tesla T10 Processor) Cuda version 3.1 CMake 2.8 I installed the OpenMM from the source using commands= ccmake -i . make make test make install everything went fine and set the paths export OPENMM_ROOT_DIR=path_to_custom_openmm_installation cmake -DGMX_OPENMM=ON then make make install The submission script used is= #!/bin/csh #PBS -l gpu=1 #PBS -l ncpus=1 #PBS -o /global/utemp/cuda-out2.out #PBS -e /global/utemp/cuda-err2.out /home/staff/software/gromacs_gpu_t/bin/mdrun-gpu -device "OpenMM:platform=Cuda,DeviceID=0,Memtest=15,**,force-device=yes" -v -deffnm /global/utemp/md for this i receive an error such as Cuda error in file '/home/staff/software/openmm_tesla/platforms/cuda/./src/kernels//bbsort.cu' in line 176 : unspecified launch failure. /bin/cat: file_loc: No such file or directory On Thu, Jan 19, 2012 at 11:41 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > aiswarya pawar wrote: > >> Szilárd, >> >> I did a memory test run yesterday and it went fine but today received an >> error. So you mean to say the tesla card version nothing to do with this >> right. >> >> > You're trying to solve multiple problems at once. You told Mark that the > normal mdrun executable (which works independently of any GPU components) > also hangs, so either your filesystem is faulty or your installation > procedure produced nonfunctional executables. > > You're posting bits and pieces of information, which makes it incredibly > hard for anyone to help you. Let's recap and try again. Please provide: > > 1. The Gromacs version you're using > 2. Description of the hardware (GPU and non-GPU components) > 3. Installation procedure for Gromacs and any of the prerequisite software > and libraries that were required, including versions > 4. The exact command(s) you're issuing, including the full script that is > causing a problem > > -Justin > > Thanks >> >> >> On Thu, Jan 19, 2012 at 11:09 PM, Szilárd Páll >> <szilard.p...@cbr.su.se<mailto: >> szilard.p...@cbr.su.se**>> wrote: >> >> That's a generic GPU kernel launch failure which can mean anything, >> from faulty hardware to bad driver to messed up installation. >> >> Does the memory test run? Try to compile/install again and see if it >> works. >> >> -- >> Szilárd >> >> >> >> On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar >> <aiswarya.pa...@gmail.com >> <mailto:aiswarya.pawar@gmail.**com<aiswarya.pa...@gmail.com>>> >> wrote: >> > when i tired running it again, i got an error as >> > >> > Cuda error in file >> > >> '/home/staff/sec/secdpal/**software/openmm_tesla/** >> platforms/cuda/./src/kernels//**bbsort.cu <http://bbsort.cu> >> <http://bbsort.cu>' >> >> > in line 176 : unspecified launch failure. >> > >> > /bin/cat: file_loc: No such file or directory >> > >> > >> > On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar >> <aiswarya.pa...@gmail.com >> <mailto:aiswarya.pawar@gmail.**com<aiswarya.pa...@gmail.com> >> >> >> >> > wrote: >> >> >> >> Has the tesla card got to do anything with the error. Am >> using Nvidia >> >> Tesla S1070 1U server. >> >> >> >> >> >> On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll >> <szilard.p...@cbr.su.se <mailto:szilard.p...@cbr.su.se**>> >> >> >> wrote: >> >>> >> >>> And sorting out where the /bin/cat error comes from because that >> is >> >>> surely not a Gromacs message! >> >>> >> >>> Cheers, >> >>> -- >> >>> Szilárd >> >>> >> >>> >> >>> >> >>> On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham >> <mark.abra...@anu.edu.au >> <mailto:mark.abra...@anu.edu.**au<mark.abra...@anu.edu.au> >> >> >> >> >>> wrote: >> >>> > On 19/01/2012 8:45 PM, aiswarya pawar wrote: >> >>> > >> >>> > Mark, >> >>> > >> >>> > THe normal mdrun also hangs thus not generating any output. >> >>> > >> >>> > >> >>> > OK. It's your problem to solve... keep simplifying stuff >> until you can >> >>> > isolate a small number of possible causes. Top of the list is >> file >> >>> > system >> >>> > availability. >> >>> > >> >>> > Mark >> >>> > >> >>> > >> >>> > >> >>> > On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham >> <mark.abra...@anu.edu.au >> <mailto:mark.abra...@anu.edu.**au<mark.abra...@anu.edu.au> >> >> >> >> >>> > wrote: >> >>> >> >> >>> >> On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com >> <mailto:aiswarya.pawar@gmail.**com <aiswarya.pa...@gmail.com>> wrote: >> >>> >> >> >>> >> Hi, >> >>> >> >> >>> >> Its going into the running mode but gets hang there for long >> hours >> >>> >> which >> >>> >> generating any data in the output file. And am not able to >> figure out >> >>> >> the >> >>> >> error file_doc. Please anyone knows what's going wrong. >> >>> >> >> >>> >> >> >>> >> No, but you should start trying to simplify what you're >> doing to see >> >>> >> where >> >>> >> the problem lies. Does normal mdrun work? >> >>> >> >> >>> >> Mark >> >>> >> >> >>> >> >> >>> >> Thanks >> >>> >> Sent from my BlackBerryŽ on Reliance Mobile, India's No. 1 >> >> Network. Go >> >>> >> for >> >>> >> it! >> >>> >> >> >>> >> -----Original Message----- >> >>> >> From: Szilárd Páll <szilard.p...@cbr.su.se >> <mailto:szilard.p...@cbr.su.se**>> >> >>> >> Sender: gmx-users-boun...@gromacs.org >> <mailto:gmx-users-bounces@**gromacs.org<gmx-users-boun...@gromacs.org> >> > >> >>> >> Date: Wed, 18 Jan 2012 14:47:59 >> >>> >> To: Discussion list for GROMACS users<gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org>**> >> >>> >> Reply-To: Discussion list for GROMACS users >> <gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>**> >> >>> >> Subject: Re: [gmx-users] mdrun-gpu error >> >>> >> >> >>> >> Hi, >> >>> >> >> >>> >> Most of those are just warnings, the only error I see there >> comes from >> >>> >> the shell, probably an error in your script. >> >>> >> >> >>> >> Cheers, >> >>> >> -- >> >>> >> Szilárd >> >>> >> >> >>> >> >> >>> >> >> >>> >> On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar >> >>> >> <aiswarya.pa...@gmail.com >> <mailto:aiswarya.pawar@gmail.**com<aiswarya.pa...@gmail.com> >> >> >> >> wrote: >> >>> >> >> >>> >> Hi users, >> >>> >> >> >>> >> Am running mdrun on gpu . I receive an error such as= >> >>> >> >> >>> >> WARNING: This run will generate roughly 38570 Mb of data >> >>> >> >> >>> >> >> >>> >> WARNING: OpenMM does not support leap-frog, will use >> velocity-verlet >> >>> >> integrator. >> >>> >> >> >>> >> >> >>> >> WARNING: OpenMM supports only Andersen thermostat with the >> >>> >> md/md-vv/md-vv-avek integrators. >> >>> >> >> >>> >> >> >>> >> WARNING: OpenMM supports only Monte Carlo barostat for pressure >> >>> >> coupling. >> >>> >> >> >>> >> >> >>> >> WARNING: OpenMM provides contraints as a combination of >> SHAKE, SETTLE >> >>> >> and >> >>> >> CCMA. Accuracy is based on the SHAKE tolerance set by the >> "shake_tol" >> >>> >> option. >> >>> >> >> >>> >> /bin/cat: file_loc: No such file or directory >> >>> >> >> >>> >> >> >>> >> and the job is running but the nothing written into .xtc, >> .trr, .edr >> >>> >> files >> >>> >> . >> >>> >> What could have gone wrong? >> >>> >> >> >>> >> -- >> >>> >> Aiswarya B Pawar >> >>> >> >> >>> >> Bioinformatics Dept, >> >>> >> Indian Institute of Science >> >>> >> Bangalore >> >>> >> >> >>> >> >> >>> >> >> >>> >> -- >> >>> >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> >>> >> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> >>> >> Please search the archive at >> >>> >> >> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> >>> >> Please don't post (un)subscribe requests to the list. Use the >> >>> >> www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> >> >>> >> Can't post? Read http://www.gromacs.org/** >> Support/Mailing_Lists <http://www.gromacs.org/Support/Mailing_Lists> >> >>> >> >> >>> >> -- >> >>> >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> >>> >> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> >>> >> Please search the archive at >> >>> >> >> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> >>> >> Please don't post (un)subscribe requests to the list. Use the >> >>> >> www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> >> >>> >> Can't post? Read http://www.gromacs.org/** >> Support/Mailing_Lists <http://www.gromacs.org/Support/Mailing_Lists> >> >>> >> >> >>> >> >> >>> >> >> >>> >> >> >>> >> >> >>> >> -- >> >>> >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> >>> >> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> >>> >> Please search the archive at >> >>> >> >> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> >>> >> Please don't post (un)subscribe requests to the list. Use the >> >>> >> www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> >> >>> >> Can't post? Read http://www.gromacs.org/** >> Support/Mailing_Lists <http://www.gromacs.org/Support/Mailing_Lists> >> >>> > >> >>> > >> >>> > >> >>> > >> >>> > -- >> >>> > Aiswarya B Pawar >> >>> > >> >>> > Bioinformatics Dept, >> >>> > Indian Institute of Science >> >>> > Bangalore >> >>> > >> >>> > >> >>> > >> >>> > >> >>> > >> >>> > >> >>> > -- >> >>> > gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> >>> > >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> >>> > Please search the archive at >> >>> > >> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> >>> > Please don't post (un)subscribe requests to the list. Use the >> >>> > www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> >> >>> > Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> >>> -- >> >>> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> >>> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> >>> Please search the archive at >> >>> >> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> >>> Please don't post (un)subscribe requests to the list. Use the >> >>> www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> >> >>> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> >> >> >> >> >> >> >> >> >> -- >> >> Aiswarya B Pawar >> >> >> >> Bioinformatics Dept, >> >> Indian Institute of Science >> >> Bangalore >> >> >> >> >> > >> > >> > >> > -- >> > Aiswarya B Pawar >> > >> > Bioinformatics Dept, >> > Indian Institute of Science >> > Bangalore >> > >> > >> > >> > -- >> > gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> > >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > Please search the archive at >> > >> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> > Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> >> > Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at >> >> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> >> >> >> >> -- >> Aiswarya B Pawar >> >> Bioinformatics Dept, >> Indian Institute of Science >> Bangalore >> >> >> > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore
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