Seems like my last message got lost because the CMakeError.log was too big, I attached that as a zip file.
If i call sysconf() without any arguments it returns 1. Sysconf(_SC_NPROCESSOR_ONLN) complains that _SC_NPROCESSOR_ONLN is not defined. Also this comes up during make, which looks like trouble: src/gromacs/gmxlib/gmx_detect_ hardware.c: In function ‘get_nthreads_hw_avail’: src/gromacs/gmxlib/gmx_detect_hardware.c:414:1: warning: implicit declaration of function ‘sysconf’ [-Wimplicit-function-declaration] I built gromacs as described in: http://www.gromacs.org/Documentation/Installation_Instructions/Cmake#MPI_build with cmake -DGMX_MPI=ON ../gromacs-src make -j 8 I did not set anything else. 2013/2/5 Roland Schulz <rol...@utk.edu> > >> On Tue, Feb 5, 2013 at 8:58 AM, Berk Hess <g...@hotmail.com> wrote: >> >> > >> > One last thing: >> > Maybe a macro is not set, but we can actually query the number of >> > processors. >> > Could you replace the conditional that gets triggered on my machine: >> > #if defined(_SC_NPROCESSORS_ONLN) >> > to >> > #if 1 >> > >> > So we can check if the actual sysconf call works or not? >> > >> > My workaround won't work without OpenMP. >> > Did you disable that manually? >> > >> > Also large file support is not turned on. >> > It seems like your build setup is somehow messed up and lot of features >> > are not found. >> > >> >> Could you post your CMakeFiles/CMakeError.log? That should show why those >> features are disabled. >> >> Roland >> >> >> > >> > Cheers, >> > >> > Berk >> > >> > >> > ---------------------------------------- >> > > Date: Tue, 5 Feb 2013 14:52:17 +0100 >> > > Subject: Re: [gmx-users] MPI oversubscription >> > > From: hypo...@googlemail.com >> > > To: gmx-users@gromacs.org >> > > >> > > 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 >> > -- >> > 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 >> -- >> 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 >> > >
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