[gmx-developers] gromacs 5.1rc1 OpenCL problem with Parrinello-Rahman

Szilárd Páll pall.szilard at gmail.com
Mon Jul 20 21:47:23 CEST 2015


Thanks Wouter, good to know! That note seems to be quite old, though and
seems to flag OSX >=10.7.4, but given that the most recent development
tools seem to be able to compile correctly, it could be that the/some bug
was fixed recently.

I don't think there's anything concrete to conclude yet, except that we
likely have to blacklist some Apple OpenCL runtime versions, but somebody
will have to investigate further. I have neither hardware nor time for
that, though.

For those interested in helping (would be much appreciated!) or tracking
the progress on this topic, I filed an issue:
http://redmine.gromacs.org/issues/1783

Cheers,

--
Szilárd

On Mon, Jul 20, 2015 at 9:08 PM, Wouter Boomsma <wb at bio.ku.dk> wrote:

> Hi,
>
> I don't know if this is in any way related, but the OpenMM community has
> had problems with the OpenCL implementation on OSX for several years
> now. From the main download page:
>
> *NOTE: Bug in recent versions of Mac OSX produces errors with the OpenMM
>> OpenCL platform*. We are currently working with Apple to resolve the
>> issue. In the meantime, if you use the OpenCL platform, we recommend that
>> you do NOT upgrade your OS beyond 10.7.4. Those running the CUDA platform
>> are unaffected. *Last updated: Nov. 21, 2012*
>
>
> Cheers,
> Wouter
>
>
> On Mon, Jul 20, 2015 at 8:07 PM, Szilárd Páll <pall.szilard at gmail.com>
> wrote:
>
>> Hi,
>>
>> At this point my guess is that the source of the issue is the particular
>> version of the Apple OpenCL runtime or compiler you have. Unfortunately,
>> our version info does not contain any OpenCL runtime/compiler version
>> information, but you should be able to query that and compare it against
>> someone else's version:
>> system_profiler | grep -A 10 OpenCL
>>
>> Cheers,
>>
>> --
>> Szilárd
>>
>> On Mon, Jul 20, 2015 at 7:50 PM, Carlo Camilloni <
>> carlo.camilloni at gmail.com> wrote:
>>
>>> Hi again,
>>>
>>> I don’t know if you had the opportunity to reproduce this bug, in the
>>> meantime I have compiled it with gcc 4.8, openMP and sse4.1,
>>> again cpu results are consistently right while OpenCL results are
>>> consistently wrong, so it looks like it is NOT a problem of Clang 6
>>> but it could be either a problem of the gpu driver or maybe OpenCL
>>> itself, I don’t know..
>>>
>>> this is the new log
>>>
>>> GROMACS version:    VERSION 5.1-rc1
>>> Precision:          single
>>> Memory model:       64 bit
>>> MPI library:        thread_mpi
>>> OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 32)
>>> GPU support:        enabled
>>> OpenCL support:     enabled
>>> invsqrt routine:    gmx_software_invsqrt(x)
>>> SIMD instructions:  SSE4.1
>>> FFT library:        fftw-3.3.4-sse2-avx
>>> RDTSCP usage:       enabled
>>> C++11 compilation:  disabled
>>> TNG support:        enabled
>>> Tracing support:    disabled
>>> Built on:           Mon 20 Jul 2015 18:21:43 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:         /opt/local/bin/gcc GNU 4.8.5
>>> C compiler flags:    -msse4.1    -Wextra -Wno-missing-field-initializers
>>> -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value
>>> -Wunused-parameter  -O3 -DNDEBUG -funroll-all-loops
>>> -fexcess-precision=fast  -Wno-array-bounds
>>> C++ compiler:       /opt/local/bin/g++ GNU 4.8.5
>>> C++ compiler flags:  -msse4.1    -Wextra -Wno-missing-field-initializers
>>> -Wpointer-arith -Wall -Wno-unused-function  -O3 -DNDEBUG -funroll-all-loops
>>> -fexcess-precision=fast  -Wno-array-bounds
>>> 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
>>>
>>>
>>> Best,
>>> Carlo
>>>
>>>
>>>
>>> On 17 Jul 2015, at 13:54, Carlo Camilloni <carlo.camilloni at gmail.com>
>>> wrote:
>>>
>>> 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>
>>> 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>
>>>> <carlo.camilloni at gmail.com>
>>>> Reply: Carlo Camilloni <carlo.camilloni at gmail.com>>
>>>> <carlo.camilloni at gmail.com>
>>>> Date: 16 Jul 2015 at 19:07:13
>>>> To: Erik Lindahl <erik.lindahl at gmail.com>> <erik.lindahl at gmail.com>
>>>> Cc: gromacs.org_gmx-developers at maillist.sys.kth.se
>>>> <gromacs.org_gmx-developers at maillist.sys.kth.se>>
>>>> <gromacs.org_gmx-developers at maillist.sys.kth.se>,
>>>> gmx-developers at gromacs.org <gmx-developers at gromacs.org>>
>>>> <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> 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>
>>>> <carlo.camilloni at gmail.com>
>>>> Reply: gmx-developers at gromacs.org <gmx-developers at gromacs.org>>
>>>> <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>>
>>>> <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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>>>> >>>
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>>>> Gromacs Developers mailing list
>>>>
>>>> * Please search the archive at
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>>>>  --
>>>> Erik Lindahl <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>
>>>> 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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>>>
>>>
>>>
>>>
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