[gmx-developers] gromacs 5.1rc1 OpenCL problem with Parrinello-Rahman
Carlo Camilloni
carlo.camilloni at gmail.com
Fri Jul 17 13:54:52 CEST 2015
Hi,
Unfortunately on the Mac Pro I am running os x 10.9.5 and the newer clang is not yet available so I cannot test it
with a different version. Erik if you have time to tell me what to change to get gromacs compiled with gcc I can give it a try
Carlo
> On 16 Jul 2015, at 20:28, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
> Hi,
>
> Philip Fowler made a recent positive report on OpenCL+AMD+Mac and he was using /usr/bin/cc Clang 6.1.0.6020053, so there may be an issue with Clang 6.0 (whatever real clang version that is...)
>
> Mark
>
> On Thu, Jul 16, 2015 at 7:20 PM Erik Lindahl <erik.lindahl at gmail.com <mailto:erik.lindahl at gmail.com>> wrote:
> Hi,
>
> The one obvious difference I can see is that you have clang 6.0.0, while at least my Macbook pro says 6.1.0.
>
> Could you check if there is any update available for the developer tools, and if so does that help?
>
> It is actually much better to use gcc since you will then also use all CPU cores. However, that requires patching a header file in /usr/include; I’ll dig up what I did there - we need to put it in the documentation anyway.
>
> Cheers,
>
> Erik
>
> From: Carlo Camilloni <carlo.camilloni at gmail.com> <mailto:carlo.camilloni at gmail.com>
> Reply: Carlo Camilloni <carlo.camilloni at gmail.com>> <mailto:carlo.camilloni at gmail.com>
> Date: 16 Jul 2015 at 19:07:13
> To: Erik Lindahl <erik.lindahl at gmail.com>> <mailto:erik.lindahl at gmail.com>
> Cc: gromacs.org_gmx-developers at maillist.sys.kth.se <mailto: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>, gmx-developers at gromacs.org <mailto:gmx-developers at gromacs.org> <gmx-developers at gromacs.org>> <mailto:gmx-developers at gromacs.org>
>
> Subject: Re: [gmx-developers] gromacs 5.1rc1 OpenCL problem with Parrinello-Rahman
>
>> 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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto:mark.j.abraham at gmail.com>>
>>>> >> To: gmx-developers at gromacs.org <mailto:gmx-developers at gromacs.org>,
>>>> >> 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
>>>> >> Message-ID:
>>>> >> <CAMNuMATveVRRyBBwn312xrY+w3M7deC2Hs3A7PZnaeugkw+VVA at mail.gmail.com <mailto: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 <mailto: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
>>
> --
> 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
> --
> Gromacs Developers mailing list
>
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