[gmx-users] FYI: How to install Gromacs 4.6.5 on Windows 7: keep cygwin packages 1.7.1-2 for OpenMPI: version 1.7.4-2 for OpenMPI is compatibel

Thu Mar 13 13:25:58 CET 2014

Hi Chris,

I've got a few questions/comments.

> 7) -DCMAKE_INSTALL_PREFIX="/cygdrive/c/Gromacs465" is the installation directory -DGMX_MPI=OFF With the second installation 10) to 13) you will replace the non-mpi mdrun.exe with one that can run on multiple cores. If you omit this step, the generated mdrun.exe will not work as it is not compatible with the current cygwin setup.

It's not clear to me what is not compatible with cygwin? Is it
thread-MPI you are referring to?
Have you tried OpenMP parallelization?

> -DGMX_PREFER_STATIC_LIBS=ON makes sure your library is found: pointing to it via -DFFTW_LIBRARY and -DFFTW_INCLUDE causes errors.

Not really:
- Using FFTW_LIBRARY/FFTW_INCLUDE is not really the appropriate way to
hint the location of FFTW; use CMAKE_PREFIX_PATH instead (see the docs
for more details).
- GMX_PREFER_STATIC_LIBS=ON just tells cmake to look for static
archives instead of dynamic libraries to link with. I think both
should work,

> -DGMX_CPU_ACCELERATION=SSE2 makes sure to select the Gromacs compatible acceleration.

Not sure what you mean by "compatible" - GROMACS 4.6 supports SSE2,
SSE4.1, AVX (128-bit+FMA/256-bit) and your CPU is an Intel Sandy
Bridge which is capable of AVX (http://goo.gl/a8vAgK). You should not
specify any SIMD/acceleration unless you are compiling for another
machine (or your compiler does not support your CPU). Instead let
CMake detect your CPU's capability and select the appropriate setting.

Cheers,
--
Szilárd

On Thu, Mar 13, 2014 at 10:20 AM, Christian Wagner
<wagner at mail.sysu.edu.cn> wrote:
>
> Dear All,
>
>
> The latest update of the cygwin OpenMPI packages (version 1.7.4-2) is fully compatible with a Gromacs 4.6.5 installation.
>
>
> Approach: update cygwin packages, then run Gromacs regression tests
> Result: all tests passed
>
>
> Regards,
> Chris Wagner
> ----- Original Message -----
>
> From: "Christian Wagner" <wagner at mail.sysu.edu.cn>
> To: gmx-users at gromacs.org
> Cc: "gromacs org gmx-users" <gromacs.org_gmx-users at maillist.sys.kth.se>
> Sent: Friday, February 28, 2014 2:12:14 PM
> Subject: Re: [gmx-users] FYI: How to install Gromacs 4.6.5 on Windows 7: keep cygwin packages 1.7.1-2 for OpenMPI
>
> Please make sure to use the OpenMPI cygwin package 1.7.1-2
> When I installed the latest upgrade, MPI troubles occurred and Gromacs mdrun was broken.
>
>
> Details:
>
> The troubles were:
> 1) MPI installation was no longer detected by cmake (when I tried rebuilding)
> 2) could no longer execute mpirun nor mpiexec (both broken like mdrun)
>
> The individual x86_64 OpenMPI cygwin packages are listed here:
> http://cygwin.com/cgi-bin2/package-grep.cgi?grep=openmpi&arch=x86_64
>
>
>
> Solution:
> After reverting to 1.7.1-2, I verified the Gromacs installation by running successfully the regression-tests.
>
>
> Chris Wagner
>
> ----- Original Message -----
> From: "Christian Wagner" <wagner at mail.sysu.edu.cn>
> To: "gromacs org gmx-users" <gromacs.org_gmx-users at maillist.sys.kth.se>
> Sent: Monday, February 24, 2014 1:06:47 PM
> Subject: [gmx-users] FYI: How to install Gromacs 4.6.5 on Windows 7
>
> Hello All,
>
> Below I summarize a cygwin installation of Gromacs 4.6.5 using FFTW 3.3.3 on a Windows 7, 64 bit SP1 system. The installation passed all the regression tests.
>
> Note:
> I give first the recipe and below explanations per point. This installation on a laptop computer (Intel Core i3 2330M (2 core, 4 threads)) may be more suitable for teaching purposes than for a serious modeler, who is looking for a high performance setup.
>
>
>
>
> Prerequisites:
>
> A) administrator privileges on the Windows computer
> B) 7-zip (or similar)
> C) cygwin 64 bit (installed are all current packages except 'audio' and 'mail')
> D) cmake 2.8.12.1
> E) MinGW (complete installation)
>
>
>
>
> all installations are done using the 64 bit version of cygwin
>
>
>
>
> Recipe:
>
> 1) download FFTW 3.3.3 and unpack
> 2) ./configure --prefix c:/fftw_3.3.3 --enable-float --enable-sse2
> 3) make
> 4) make install
> 5) link lib location to PATH
>
> 6) download Gromacs 4.6.5 and unpack
> 7) cmake .. -DCMAKE_INSTALL_PREFIX="/cygdrive/c/Gromacs465" -DGMX_X11=OFF -DGMX_GPU=OFF -DGMX_MPI=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_CPU_ACCELERATION=SSE2 -DBUILD_SHARED_LIBS=NO
> 8) make
> 9) make install
>
> 10) delete build
> 11) cmake .. -DCMAKE_INSTALL_PREFIX="/cygdrive/c/Gromacs465" -DGMX_GPU=OFF -DGMX_MPI=ON -DGMX_PREFER_STATIC_LIBS=ON -DGMX_CPU_ACCELERATION=SSE2
> 12) make
> 13) make install-mdrun
>
> 14) find mdrun_mpi.exe
> 15) replace mdrun.exe with mdrun_mpi.exe
> 16) rename mdrun_mpi.exe to mdrun.exe
>
>
>
> Verify installation:
> 17) download regression tests and unpack
> 18) source /cygdrive/c/Gromacs465/bin/GMXRC
> 19) ./gmxtest.pl all
>
>
>
>
> Explanations:
>
> A) Windows permissions frequently interfere with the installation: you need to ensure that there is actually read and write access at the locations the installations take place (despite being administrator: if you need to confirm administrator rights etc, the installation will stop). You may also need to reapply the security settings during the installation and propagate the permission along the tree (this issue come up especially at point 9)). Make sure to install into root directories, to prevent difficulties handling long file names. If you want to run the programs not only from the cygwin terminal but also from a systems command prompt, you will also need to add the different paths of the executables' locations to the system environment variable.
> B) 7-zip is free ware and can handle not only .zip but also .tar and .gz formats: http://www.7-zip.org/
> C) When installing cygwin make sure that there are no spaces or special characters in the directory as this will cause compatibility issues: best to install into the root as indicated during the cygwin installation setup. After installation link the OpenMPI /bin to PATH and the OpenMPI /lib to LD_LIBRARY_PATH This entire cygwin installation will take many hours to download and to install (overnight), it may be best to do it in smaller steps http://cygwin.com/
> D) After installation link cmake to PATH The graphical interface did not work for me, so I used the command line: http://www.cmake.org/
> E) The interface requires quite some clicking to get all the packages selected. After installation link MinGW to PATH http://www.mingw.org/wiki/Getting_Started
>
> 1) The precompiled dll's did not work for me, so I installed FFTW using cygwin http://www.fftw.org/ unpack it into the root, e.g. C:/fftw-3.3.3 and cd to this location.
> 2) Here C:/fftw_3.3.3 is the installation directory --enable-float gives single digit precision, which is necessary for Gromacs 4.6.5 --enable-sse2 makes sure Gromacs 4.6.5 compatible acceleration is used.
> 5) Ensure the library will be found
>
> 6) Unpack it into the root e.g. C:/Gromacs then add a build directory e.g. C:/Gromacs/Gromabld then cd into this build directory. If you choose another location beware of the troubles indicated in A) http://www.gromacs.org/Downloads
> 7) -DCMAKE_INSTALL_PREFIX="/cygdrive/c/Gromacs465" is the installation directory -DGMX_MPI=OFF With the second installation 10) to 13) you will replace the non-mpi mdrun.exe with one that can run on multiple cores. If you omit this step, the generated mdrun.exe will not work as it is not compatible with the current cygwin setup. -DGMX_PREFER_STATIC_LIBS=ON makes sure your library is found: pointing to it via -DFFTW_LIBRARY and -DFFTW_INCLUDE causes errors. -DGMX_CPU_ACCELERATION=SSE2 makes sure to select the Gromacs compatible acceleration.
> 8) You may need to reapply the security permissions c.f. A) then continue with make. You may need to add #define HAVE_SYS_TIME_H at the very top of the file impl.h
> 9) When Gromacs is installed the resulting folder hierarchy causes security permission troubles, c.f. A) reapply the permissions until the folder tree is established. This also means that 'make install' needs to be typed in again (on my system: more than ten times).
>
> 10) Now the mpi compatible mdrun_mpi.exe is being built: delete all content of the build directory, e.g. the contents of C:/Gromacs465/Gromabld
> 11) Similar to 7) Note that MPI is ON. Note that OpenMPI needs to be linked to PATH and LD_LIBRARY_PATH as indicated above in C)
> 12) You may need to adjust permissions c.f. A)
> 13) Only reinstall mdrun
>
> 14) On my system the mdrun_mpi_exe was in C:/cygwin64/usr/local/gromacs/bin
> 15) and 16) If you do not copy and rename mdrun_mpi.exe to the Gromacs installation C:/Gromacs465/bin then you will need to point to this mdrun_mpi.exe each time you want to use it (the mdrun.exe which is in C:/Gromacs465/bin from steps 7) to 9) is not compatible with the current cygwin installation).
>
>
> 17) Put the unpacked http://gerrit.gromacs.org/download/regressiontests-4.6.5.tar.gz into a root folder e.g. C:/GromacsTest/
> 18) cd into the regressiontests-4.6.5 directory e.g. C:/GromacsTest/regressiontests-4.6.5 then get access to Gromacs by sourcing it
> 19) more infos on testing http://www.gromacs.org/Documentation/Installation_Instructions?highlight=install#4.12._Testing_GROMACS_for_correctness
>
>
> Special thanks to Mark (Gromacs) and Matteo (FFTW) for their tips. Please, amend any errors.
> Happy biocomputing,
> Chris Wagner
>
>
>
>
>
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