On Wed, Feb 6, 2013 at 2:35 PM, Roland Schulz <rol...@utk.edu> wrote:
> > On Tue, Feb 5, 2013 at 8:52 AM, Christian H. <hypo...@googlemail.com>wrote: > >> Head of .log: >> >> Gromacs version: VERSION 5.0-dev-20121213-e1fcb0a-dirty >> > > Is it on purpose that you use version 5.0 and not 4.6? Unless you plan > development I suggest to use 4.6 (git checkout release-4-6) > I can reproduce your problem with 5.0. We haven't tested 5.0 much lately > because we were so busy with 4.6. > If you want to use 5.0 you can take the version from here: https://gerrit.gromacs.org/#/c/2132/. This fixes the problems. Roland 2013/2/5 Berk Hess <g...@hotmail.com> >> >> > >> > OK, then this is an unhandled case. >> > Strange, because I am also running OpenSUSE 12.2 with the same CPU, but >> > use gcc 4.7.1. >> > >> > I will file a bug report on redmine. >> > Could you also post the header of md.log which gives all configuration >> > information? >> > >> > To make it work for now, you can insert immediately after #ifdef >> > GMX_OMPENMP: >> > if (ret <= 0) >> > { >> > ret = gmx_omp_get_num_procs(); >> > } >> > >> > >> > Cheers, >> > >> > Berk >> > >> > ---------------------------------------- >> > > Date: Tue, 5 Feb 2013 14:27:44 +0100 >> > > Subject: Re: [gmx-users] MPI oversubscription >> > > From: hypo...@googlemail.com >> > > To: gmx-users@gromacs.org >> > > >> > > None of the variables referenced here are set on my system, the print >> > > statements are never executed. >> > > >> > > What I did: >> > > >> > > printf("Checking which processor variable is set"); >> > > #if defined(_SC_NPROCESSORS_ONLN) >> > > ret = sysconf(_SC_NPROCESSORS_ONLN); >> > > printf("case 1 ret = %d\n",ret); >> > > #elif defined(_SC_NPROC_ONLN) >> > > ret = sysconf(_SC_NPROC_ONLN); >> > > printf("case 2 ret = %d\n",ret); >> > > #elif defined(_SC_NPROCESSORS_CONF) >> > > ret = sysconf(_SC_NPROCESSORS_CONF); >> > > printf("case 3 ret = %d\n",ret); >> > > #elif defined(_SC_NPROC_CONF) >> > > ret = sysconf(_SC_NPROC_CONF); >> > > printf("case 4 ret = %d\n",ret); >> > > #endif /* End of check for sysconf argument values */ >> > > >> > > >From /etc/issue: >> > > Welcome to openSUSE 12.2 "Mantis" - Kernel \r (\l) >> > > >From uname -a: >> > > Linux kafka 3.4.11-2.16-desktop #1 SMP PREEMPT Wed Sep 26 17:05:00 UTC >> > 2012 >> > > (259fc87) x86_64 x86_64 x86_64 GNU/Linux >> > > >> > > >> > > >> > > 2013/2/5 Berk Hess <g...@hotmail.com> >> > > >> > > > >> > > > Hi, >> > > > >> > > > This is the same cpu I have in my workstation and this case should >> not >> > > > cause any problems. >> > > > >> > > > Which operating system and version are you using? >> > > > >> > > > If you know a bit about programming, could you check what goes >> wrong in >> > > > get_nthreads_hw_avail >> > > > in src/gmxlib/gmx_detect_hardware.c ? >> > > > Add after the four "ret =" at line 434, 436, 438 and 440: >> > > > printf("case 1 ret = %d\n",ret); >> > > > and replace 1 by different numbers. >> > > > Thus you can check if one of the 4 cases returns 0 or none of the >> cases >> > > > is called. >> > > > >> > > > Cheers, >> > > > >> > > > Berk >> > > > >> > > > >> > > > ---------------------------------------- >> > > > > Date: Tue, 5 Feb 2013 13:45:02 +0100 >> > > > > Subject: Re: [gmx-users] MPI oversubscription >> > > > > From: hypo...@googlemail.com >> > > > > To: gmx-users@gromacs.org >> > > > > >> > > > > >From the .log file: >> > > > > >> > > > > Present hardware specification: >> > > > > Vendor: GenuineIntel >> > > > > Brand: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz >> > > > > Family: 6 Model: 42 Stepping: 7 >> > > > > Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr >> > > > nonstop_tsc >> > > > > pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 >> > tdt >> > > > > Acceleration most likely to fit this hardware: AVX_256 >> > > > > Acceleration selected at GROMACS compile time: AVX_256 >> > > > > >> > > > > Table routines are used for coulomb: FALSE >> > > > > Table routines are used for vdw: FALSE >> > > > > >> > > > > >> > > > > >From /proc/cpuinfo (8 entries like this in total): >> > > > > >> > > > > processor : 0 >> > > > > vendor_id : GenuineIntel >> > > > > cpu family : 6 >> > > > > model : 42 >> > > > > model name : Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz >> > > > > stepping : 7 >> > > > > microcode : 0x28 >> > > > > cpu MHz : 1600.000 >> > > > > cache size : 8192 KB >> > > > > physical id : 0 >> > > > > siblings : 8 >> > > > > core id : 0 >> > > > > cpu cores : 4 >> > > > > apicid : 0 >> > > > > initial apicid : 0 >> > > > > fpu : yes >> > > > > fpu_exception : yes >> > > > > cpuid level : 13 >> > > > > wp : yes >> > > > > flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca >> > > > > cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe >> > syscall nx >> > > > > rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl >> xtopology >> > > > > nonstop_tsc aperfmper >> > > > > f pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr >> > pdcm >> > > > pcid >> > > > > sse4_1 sse4_2 popcnt tsc_deadline_timer aes xsave avx lahf_lm ida >> > arat >> > > > epb >> > > > > xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid >> > > > > bogomips : 6784.04 >> > > > > clflush size : 64 >> > > > > cache_alignment : 64 >> > > > > address sizes : 36 bits physical, 48 bits virtual >> > > > > power management: >> > > > > >> > > > > >> > > > > It also does not work on the local cluster, the output in the .log >> > file >> > > > is: >> > > > > >> > > > > Detecting CPU-specific acceleration. >> > > > > Present hardware specification: >> > > > > Vendor: AuthenticAMD >> > > > > Brand: AMD Opteron(TM) Processor 6220 >> > > > > Family: 21 Model: 1 Stepping: 2 >> > > > > Features: aes apic avx clfsh cmov cx8 cx16 fma4 htt lahf_lm >> > misalignsse >> > > > mmx >> > > > > msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a >> > sse4.1 >> > > > > sse4.2 ssse3 xop >> > > > > Acceleration most likely to fit this hardware: AVX_128_FMA >> > > > > Acceleration selected at GROMACS compile time: AVX_128_FMA >> > > > > Table routines are used for coulomb: FALSE >> > > > > Table routines are used for vdw: FALSE >> > > > > >> > > > > I am not too sure about the details for that setup, but the brand >> > looks >> > > > > about right. >> > > > > Do you need any other information? >> > > > > Thanks for looking into it! >> > > > > >> > > > > 2013/2/5 Berk Hess <g...@hotmail.com> >> > > > > >> > > > > > >> > > > > > Hi, >> > > > > > >> > > > > > This looks like our CPU detection code failed and the result is >> not >> > > > > > handled properly. >> > > > > > >> > > > > > What hardware are you running on? >> > > > > > Could you mail the 10 lines from the md.log file following: >> > "Detecting >> > > > > > CPU-specific acceleration."? >> > > > > > >> > > > > > Cheers, >> > > > > > >> > > > > > Berk >> > > > > > >> > > > > > >> > > > > > ---------------------------------------- >> > > > > > > Date: Tue, 5 Feb 2013 11:38:53 +0100 >> > > > > > > From: hypo...@googlemail.com >> > > > > > > To: gmx-users@gromacs.org >> > > > > > > Subject: [gmx-users] MPI oversubscription >> > > > > > > >> > > > > > > Hi, >> > > > > > > >> > > > > > > I am using the latest git version of gromacs, compiled with >> gcc >> > > > 4.6.2 and >> > > > > > > openmpi 1.6.3. >> > > > > > > I start the program using the usual mpirun -np 8 mdrun_mpi ... >> > > > > > > This always leads to a warning: >> > > > > > > >> > > > > > > Using 1 MPI process >> > > > > > > WARNING: On node 0: oversubscribing the available 0 logical >> CPU >> > > > cores per >> > > > > > > node with 1 MPI processes. >> > > > > > > >> > > > > > > Checking the processes confirms that there is only one of the >> 8 >> > > > available >> > > > > > > cores used. >> > > > > > > Running mdrun_mpi with an additional debug -1: >> > > > > > > >> > > > > > > Detected 0 processors, will use this as the number of >> supported >> > > > hardware >> > > > > > > threads. >> > > > > > > hw_opt: nt 0 ntmpi 0 ntomp 1 ntomp_pme 1 gpu_id '' >> > > > > > > 0 CPUs detected, but 8 was returned by CPU_COUNTIn >> > > > gmx_setup_nodecomm: >> > > > > > > hostname 'myComputerName', hostnum 0 >> > > > > > > ... >> > > > > > > 0 CPUs detected, but 8 was returned by CPU_COUNTOn rank 0, >> > thread 0, >> > > > core >> > > > > > > 0 the affinity setting returned 0 >> > > > > > > >> > > > > > > I also made another try by compiling gromacs using some >> > experimental >> > > > > > > version of gcc 4.8, which did not help in this case. >> > > > > > > Is this a known problem? Obviously gromacs detects the right >> > value >> > > > with >> > > > > > > CPU_COUNT, why is it not just taking that value? >> > > > > > > >> > > > > > > >> > > > > > > Best regards, >> > > > > > > Christian >> > > > > > > -- >> > > > > > > gmx-users mailing list gmx-users@gromacs.org >> > > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > > > > > > * Please search the archive at >> > > > > > 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 >> > > > > > -- >> > > > > > gmx-users mailing list gmx-users@gromacs.org >> > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > > > > > * Please search the archive at >> > > > > > 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 >> > > > > > >> > > > > -- >> > > > > gmx-users mailing list gmx-users@gromacs.org >> > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > > > > * Please search the archive at >> > > > 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 >> > > > -- >> > > > gmx-users mailing list gmx-users@gromacs.org >> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > > > * Please search the archive at >> > > > 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 >> > > > >> > > -- >> > > gmx-users mailing list gmx-users@gromacs.org >> > > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > > * Please search the archive at >> > 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 >> > -- >> > gmx-users mailing list gmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > * Please search the archive at >> > 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 >> > >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> 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 >> >> >> >> >> > > > -- > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov > 865-241-1537, ORNL PO BOX 2008 MS6309 > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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