And if the zip file did not get through: http://de.pastebin.ca/2311103
2013/2/6 Christian H. <hypo...@googlemail.com> > 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 >>> >> >> > -- 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? 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