[gmx-users] MPI oversubscription
Berk Hess
gmx3 at hotmail.com
Tue Feb 5 14:39:56 CET 2013
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: hypolit at googlemail.com
> To: gmx-users at 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 <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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