[gmx-developers] gromacs 5.1rc1 OpenCL problem with Parrinello-Rahman
Robert McGibbon
rmcgibbo at gmail.com
Mon Jul 20 22:00:18 CEST 2015
The Apple OpenCL bugs that were relevant for OpenMM were fixed in OSX
10.10.3.
-Robert
On Mon, Jul 20, 2015 at 12:47 PM, Szilárd Páll <pall.szilard at gmail.com>
wrote:
> 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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>>>>> --
>>>>> 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
>>>>> --
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>>>>
>>>>
>>>>
>>>>
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