[gmx-developers] gromacs 5.1rc1 OpenCL problem with Parrinello-Rahman
Carlo Camilloni
carlo.camilloni at gmail.com
Thu Jul 16 19:07:16 CEST 2015
Hi Erik,
here it is:
GROMACS version: VERSION 5.1-rc1
Precision: single
Memory model: 64 bit
MPI library: none
OpenMP support: disabled
GPU support: enabled
OpenCL support: enabled
invsqrt routine: gmx_software_invsqrt(x)
SIMD instructions: AVX_256
FFT library: fftw-3.3.4-sse2-avx
RDTSCP usage: enabled
C++11 compilation: disabled
TNG support: enabled
Tracing support: disabled
Built on: Thu 16 Jul 2015 09:34:14 BST
Built by: carlo@ [CMAKE]
Build OS/arch: Darwin 13.4.0 x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Xeon(R) CPU E5-1650 v2 @ 3.50GHz
Build CPU family: 6 Model: 62 Stepping: 4
Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc Clang 6.0.0.6000057
C compiler flags: -mavx -Wall -Wno-unused -Wunused-value -Wunused-parameter -Wno-unknown-pragmas -O3 -DNDEBUG
C++ compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ Clang 6.0.0.6000057
C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -Wno-unknown-pragmas -O3 -DNDEBUG
Boost version: 1.58.0 (external)
OpenCL include dir: /System/Library/Frameworks/OpenCL.framework
OpenCL library: /System/Library/Frameworks/OPENCL.framework
OpenCL version: 1.2
Running on 1 node with total 12 logical cores, 2 compatible GPUs
Hardware detected:
CPU info:
Vendor: GenuineIntel
Brand: Intel(R) Xeon(R) CPU E5-1650 v2 @ 3.50GHz
Family: 6 model: 62 stepping: 4
CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: AVX_256
GPU info:
Number of GPUs detected: 2
#0: name: AMD Radeon HD - FirePro D500 Compute Engine, vendor: AMD, device version: OpenCL 1.2 , stat: compatible
#1: name: AMD Radeon HD - FirePro D500 Compute Engine, vendor: AMD, device version: OpenCL 1.2 , stat: compatible
Carlo
> On 16 Jul 2015, at 18:59, Erik Lindahl <erik.lindahl at gmail.com> wrote:
>
> Hi Carlo,
>
> IIRC, I managed to get it working on a Mac Pro with AMD Firepro D300 GPUs. Please post the contents of the top of your logfile (where it says everything about the compilers & config), and mention what hardware you tried it on - then we’ll see if we can reproduce it.
>
> Cheers,
>
> Erik
>
> From: Carlo Camilloni <carlo.camilloni at gmail.com> <mailto:carlo.camilloni at gmail.com>
> Reply: gmx-developers at gromacs.org <gmx-developers at gromacs.org>> <mailto:gmx-developers at gromacs.org>
> Date: 16 Jul 2015 at 18:52:21
> To: gromacs.org_gmx-developers at maillist.sys.kth.se <gromacs.org_gmx-developers at maillist.sys.kth.se>> <mailto:gromacs.org_gmx-developers at maillist.sys.kth.se>
> Subject: Re: [gmx-developers] gromacs 5.1rc1 OpenCL problem with Parrinello-Rahman
>
>> Hi,
>>
>> I tested the OpenCL kernel on my macbook (nvidia gpu) and here it produces the correct forces,
>> so it could be a problem related to amd+osx, or maybe to some specific compiler/os version
>>
>> Carlo
>>
>>
>> > On 15 Jul 2015, at 17:42, Carlo Camilloni <carlo.camilloni at gmail.com> wrote:
>> >
>> > Hi,
>> >
>> > these are the tests that fail:
>> >
>> > FAILED. Check checkpot.out (12 errors), checkforce.out (3516 errors) file(s) in dd121 for dd121
>> > FAILED. Check checkpot.out (10 errors), checkforce.out (4027 errors) file(s) in nbnxn-energy-groups for nbnxn-energy-groups
>> > FAILED. Check checkpot.out (26 errors), checkforce.out (2998 errors) file(s) in nbnxn-free-energy for nbnxn-free-energy
>> > FAILED. Check checkpot.out (26 errors), checkforce.out (2998 errors) file(s) in nbnxn-free-energy-vv for nbnxn-free-energy-vv
>> > FAILED. Check checkpot.out (11 errors), checkforce.out (4039 errors) file(s) in nbnxn-ljpme-geometric for nbnxn-ljpme-geometric
>> > FAILED. Check checkpot.out (14 errors), checkforce.out (52 errors) file(s) in nbnxn-ljpme-LB for nbnxn-ljpme-LB
>> > FAILED. Check checkpot.out (14 errors), checkforce.out (52 errors) file(s) in nbnxn-ljpme-LB-geometric for nbnxn-ljpme-LB-geometric
>> > FAILED. Check checkpot.out (10 errors), checkforce.out (4029 errors) file(s) in nbnxn-vdw-force-switch for nbnxn-vdw-force-switch
>> > FAILED. Check checkpot.out (10 errors), checkforce.out (4032 errors) file(s) in nbnxn-vdw-potential-switch for nbnxn-vdw-potential-switch
>> > FAILED. Check checkpot.out (4 errors), checkforce.out (250 errors) file(s) in nbnxn-vdw-potential-switch-argon for nbnxn-vdw-potential-switch-argon
>> > FAILED. Check checkpot.out (10 errors), checkforce.out (4027 errors) file(s) in nbnxn_pme for nbnxn_pme
>> > FAILED. Check checkpot.out (10 errors), checkforce.out (4027 errors) file(s) in nbnxn_pme_order5 for nbnxn_pme_order5
>> > FAILED. Check checkpot.out (10 errors), checkforce.out (4027 errors) file(s) in nbnxn_pme_order6 for nbnxn_pme_order6
>> > FAILED. Check checkpot.out (9 errors), checkforce.out (4028 errors) file(s) in nbnxn_rf for nbnxn_rf
>> > FAILED. Check checkpot.out (2 errors), checkforce.out (4 errors) file(s) in nbnxn_rzero for nbnxn_rzero
>> > FAILED. Check mdrun.out, md.log file(s) in nbnxn_vsite for nbnxn_vsite
>> > FAILED. Check checkpot.out (13 errors), checkforce.out (15512 errors) file(s) in octahedron for octahedron
>> > FAILED. Check mdrun.out, md.log file(s) in position-restraints for position-restraints
>> > FAILED. Check mdrun.out, md.log file(s) in pull_constraint for pull_constraint
>> > FAILED. Check checkpot.out (10 errors), checkforce.out (4021 errors) file(s) in pull_cylinder for pull_cylinder
>> > FAILED. Check checkpot.out (11 errors), checkforce.out (39054 errors) file(s) in swap_x for swap_x
>> > FAILED. Check checkpot.out (11 errors), checkforce.out (39053 errors) file(s) in swap_y for swap_y
>> > FAILED. Check checkpot.out (12 errors), checkforce.out (39054 errors) file(s) in swap_z for swap_z
>> > 23 out of 60 complex tests FAILED
>> > FAILED. Check mdrun.out, md.log file(s) in expanded for expanded
>> > FAILED. Check mdrun.out, md.log file(s) in transformAtoB for transformAtoB
>> > 2 out of 10 freeenergy tests FAILED
>> >
>> >
>> > Carlo
>> >
>> >
>> >>
>> >>
>> >> Message: 4
>> >> Date: Wed, 15 Jul 2015 15:35:13 +0000
>> >> From: Mark Abraham <mark.j.abraham at gmail.com>
>> >> To: gmx-developers at gromacs.org,
>> >> gromacs.org_gmx-developers at maillist.sys.kth.se
>> >> Subject: Re: [gmx-developers] gromacs 5.1rc1 OpenCL problem with
>> >> Parrinello-Rahman
>> >> Message-ID:
>> >> <CAMNuMATveVRRyBBwn312xrY+w3M7deC2Hs3A7PZnaeugkw+VVA at mail.gmail.com>
>> >> Content-Type: text/plain; charset="utf-8"
>> >>
>> >> Hi,
>> >>
>> >> Thanks. If a difference of that magnitude can be seen, then it should also
>> >> show up when running the regressiontests (e.g. cmake
>> >> -DREGRESSIONTEST_DOWNLOAD=on and then make check) as a failure
>> >> of complex/nbnxn-ljpme-LB (which is the only P-R test that can run on the
>> >> GPU). If other tests fail, then the problem is actually more widespread.
>> >>
>> >> It may be that there is some issue with some part of the Mac+clang+OpenCL
>> >> stack - we didn't target it during development, and at the last minute when
>> >> Erik was unexpectedly able to get it to compile. I don't know if he got
>> >> tests to pass. Erik?
>> >>
>> >> Mark
>> >>
>> >> On Wed, Jul 15, 2015 at 5:22 PM Carlo Camilloni <carlo.camilloni at gmail.com>
>> >> wrote:
>> >>
>> >>>
>> >>> Dear Mark and Szilard,
>> >>>
>> >>> thanks for your answer. I filed a bug in redmine but in the meantime I was
>> >>> running more tests and I am a bit scared by what I found:
>> >>>
>> >>> what I have done is the following I have performed a single step run with
>> >>> gmx51-rc1 compiled with cuda, again clang and so on
>> >>> and compared the forces on the first step with -nb cpu or not (I am using
>> >>> -pforce 1), the forces are identical:
>> >>>
>> >>> ie.:
>> >>>
>> >>> cuda-gpu
>> >>>
>> >>> step 0 atom 1 x 3.940 5.612 2.226 force 1.90839e+03
>> >>> step 0 atom 2 x 3.852 5.659 2.211 force 4.24845e+02
>> >>> step 0 atom 3 x 3.979 5.665 2.303 force 6.89472e+02
>> >>> step 0 atom 4 x 3.992 5.610 2.139 force 7.42053e+02
>> >>>
>> >>>
>> >>> cpu:
>> >>>
>> >>> step 0 atom 1 x 3.940 5.612 2.226 force 1.90839e+03
>> >>> step 0 atom 2 x 3.852 5.659 2.211 force 4.24845e+02
>> >>> step 0 atom 3 x 3.979 5.665 2.303 force 6.89472e+02
>> >>> step 0 atom 4 x 3.992 5.610 2.139 force 7.42053e+02
>> >>>
>> >>> if I do the same test on the version compiled with OpenCL
>> >>>
>> >>> cpu:
>> >>>
>> >>> (the former are done on my macbook pro avx2_256 this latter on a MacPro
>> >>> avx_256, this should
>> >>> explain the small differences in the forces)
>> >>>
>> >>> step 0 atom 1 x 3.940 5.612 2.226 force 1.90838e+03
>> >>> step 0 atom 2 x 3.852 5.659 2.211 force 4.24848e+02
>> >>> step 0 atom 3 x 3.979 5.665 2.303 force 6.89470e+02
>> >>> step 0 atom 4 x 3.992 5.610 2.139 force 7.42043e+02
>> >>>
>> >>> opencl-gpu:
>> >>> step 0 atom 1 x 3.940 5.612 2.226 force 1.48597e+03
>> >>> step 0 atom 2 x 3.852 5.659 2.211 force 6.26942e+02
>> >>> step 0 atom 3 x 3.979 5.665 2.303 force 8.44032e+02
>> >>> step 0 atom 4 x 3.992 5.610 2.139 force 7.92786e+02
>> >>>
>> >>> I am afraid there is something wrong in OpenCL kernels.
>> >>>
>> >>> I am using the topol-nvt-nogen.tpr I have uploaded on redmine.
>> >>>
>> >>> Best,
>> >>> Carlo
>> >>>
>> >>>
>> >>>
>> >>> --
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> --
> Erik Lindahl <erik.lindahl at gmail.com <mailto:erik.lindahl at gmail.com>>
> Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm University
> Professor of Theoretical biophysics, Dept. Theoretical Physics, Royal Inst. Technology
> Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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