[gmx-users] MPI oversubscription

Tue Feb 5 14:27:44 CET 2013

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 <gmx3 at 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: hypolit at googlemail.com
> > To: gmx-users at 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 <gmx3 at 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: hypolit at googlemail.com
> > > > To: gmx-users at 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
> > > > --
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