Head of .log: Gromacs version: VERSION 5.0-dev-20121213-e1fcb0a-dirty GIT SHA1 hash: e1fcb0a3d2768a8bb28c2e4e8012123ce773e18c (dirty) Precision: single MPI library: MPI OpenMP support: disabled GPU support: disabled invsqrt routine: gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library: fftw-3.3.2-sse2 Large file support: disabled RDTSCP usage: enabled Built on: Tue Feb 5 10:58:32 CET 2013 Built by: christian@k [CMAKE] Build OS/arch: Linux 3.4.11-2.16-desktop x86_64 Build CPU vendor: GenuineIntel Build CPU brand: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz Build CPU family: 6 Model: 42 Stepping: 7 Build CPU 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 C compiler: /home/christian/opt/bin/mpicc GNU gcc (GCC) 4.8.0 20120618 (experimental) C compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG C++ compiler: /home/christian/opt/bin/mpiCC GNU g++ (GCC) 4.8.0 20120618 (experimental) C++ compiler flags: -mavx -std=c++0x -Wextra -Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG
I will try your workaround, thanks! 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