[gmx-users] Re: gInstallation Problems with Gromacs4.6

[Abhishek Acharya]

Hello Mark
Sorry for the misunderstanding. Actually i did not provide any extra flags
to cmake. I generally edit the CMakeCache.txt file to provide the proper
paths. I somehow felt that was easier to do. I didn't think that could
lead to errors. I have installed gromacs 4.6 on multiple systems using the
same procedure, same mpi and fftw versions,  using shared libraries, but
only on HPC  i got the mentioned error. So you can imagine my surprise on
getting such an error.  And i was more surprised when it got configured
successfully on disabling the shared library flag. If there is problem
with cmake then i expect it, to give the same error irrespective of
whether i enable shared libraries or not. Just my thoughts.

With Regards
Abhishek


>

 By asking how you "calling cmake" I mean that cmake takes a number of
> command-line options, and since using those inappropriately (or not
> calling
> the right MPI wrapper compiler) might cause symptoms like yours, we need
> more complete information to have a chance of helping solve your problem.
> Christoph also asked for your cmake command line.
>
> Mark
>
> On Mon, Mar 4, 2013 at 9:04 PM, Abhishek Acharya
> <aacharya at iitk.ac.in>wrote:
>
>> > OK, but that still might not be fixing the real problem, which might
>> be
>> > starting with how you are calling cmake in the first place.
>> >
>> > Mark
>>
>>  Actually, i called the cmake-2.8.10 which i had installed in my home
>> directory as the one installed on the cluster was an old version.
>> so i cd to the cmake-build directory and gave the full path to the cmake
>> executable.
>>  /home/aacharya/softwares/cmake-2.8.10.2/bin/cmake ..
>>  I don't understand how this could have caused any installation problem.
>> Before this i also tried to use the older version cmake installed on the
>> cluster but that also gave me the same error.
>> In any case, gromacs4.6 got installed properly by disabling shared
>> libraries and is up and running. Though i would be interested in knowing
>> if its possible to remove this error in any other way.
>>
>> with regards
>> Abhishek
>>
>>
>> >
>> > On Sat, Mar 2, 2013 at 7:20 AM, Abhishek Acharya
>> > <aacharya at iitk.ac.in>wrote:
>> >
>> >> >> Date: Fri, 1 Mar 2013 23:59:36 +0530
>> >> >> From: "Abhishek Acharya" <aacharya at iitk.ac.in>
>> >> >> Subject: [gmx-users] Installation Problems with Gromacs4.6
>> >> >> To: "gromacs maillist" <gmx-users at gromacs.org>
>> >> >> Message-ID:
>> >> >>         <
>> 2ca7063e41d6ddfa7ea411dc3cfe3ad3.squirrel at webmail.iitk.ac.in>
>> >> >> Content-Type: text/plain;charset=iso-8859-1
>> >> >>
>> >> >> Hello Gromacs Users.
>> >> >> I have been trying to install Gromacs4.6 on our HPC facility. I
>> think
>> >> I
>> >> >> have correctly provided all the necessary mpi and fftw library
>> paths.
>> >> >> But
>> >> >> when i try to run configure it gives me the following error:
>> >> >>
>> >> >>  CMake Error at cmake/FindFFTW.cmake:105 (message):
>> >> >>    Could not find fftwf_plan_r2r_1d in
>> >> >>    /home/aacharya/softwares/fftw-3.3.3/lib/libfftw3f.so, take a
>> look
>> >> at
>> >> >> the
>> >> >>    error message in
>> >> >>
>>  /home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeError.log
>> >> >> to
>> >> >>    find out what went wrong.  If you are using a static lib (.a)
>> make
>> >> >> sure
>> >> >> you
>> >> >>    have specified all dependencies of fftw3f in FFTWF_LIBRARY by
>> hand
>> >> >> (e.g.
>> >> >>    -DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
>> >> >>  Call Stack (most recent call first):
>> >> >>    CMakeLists.txt:894 (find_package)
>> >> >>
>> >> >> As suggested here I looked into the CMakeError.log file of which I
>> >> can't
>> >> >> make any sense.
>> >> >>
>> >> >> Source file was:
>> >> >> #include <mpi.h>
>> >> >> int main(void) {
>> >> >>   void* buf;
>> >> >>   MPI_Allreduce(MPI_IN_PLACE, buf, 10, MPI_FLOAT, MPI_SUM,
>> >> >> MPI_COMM_WORLD);
>> >> >> }
>> >> >> Determining if the function fftwf_plan_r2r_1d exists in the
>> >> >> /home/aacharya/softwares/fftw-3.3.3/lib failed with the following
>> >> >> output:
>> >> >> Change Dir:
>> >> >> /home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp
>> >> >>
>> >> >> Run Build Command:/usr/bin/gmake "cmTryCompileExec2668319475/fast"
>> >> >> /usr/bin/gmake -f
>> >> CMakeFiles/cmTryCompileExec2668319475.dir/build.make
>> >> >> CMakeFiles/cmTryCompileExec2668319475.dir/build
>> >> >> gmake[1]: Entering directory
>> >> >> `/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
>> >> >> /home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E
>> >> >> cmake_progress_report
>> >> >>
>> >>
>> /home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp/CMakeFiles
>> >> >> 1
>> >> >> Building C object
>> >> >> CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
>> >> >> /usr/bin/cc   -Wextra -Wno-missing-field-initializers
>> >> -Wno-sign-compare
>> >> >> -Wall -Wno-unused -Wunused-value
>> >> >> -DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d   -o
>> >> >> CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
>> >> -c
>> >> >> /home/aacharya/softwares/cmake-2.8.10.2/Modules/CheckFunctionExists.c
>> >> >> Linking C executable cmTryCompileExec2668319475
>> >> >> /home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E
>> >> cmake_link_script
>> >> >> CMakeFiles/cmTryCompileExec2668319475.dir/link.txt --verbose=1
>> >> >> /usr/bin/cc   -Wextra -Wno-missing-field-initializers
>> >> -Wno-sign-compare
>> >> >> -Wall -Wno-unused -Wunused-value
>> >> >> -DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d
>> >> >> -L/home/aacharya/softwares/fftw-3.3.3/lib
>> >> >> CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
>> -o
>> >> >> cmTryCompileExec2668319475 -rdynamic -lm
>> >> > Strange, there is supposed to be a "-lfftw3f" before "-lm". Can you
>> >> > tell us what your cmake command line was?
>> >> >
>> >> >> CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o:
>> In
>> >> >> function `main':
>> >> >> CheckFunctionExists.c:(.text+0x15): undefined reference to
>> >> >> `fftwf_plan_r2r_1d'
>> >> >> collect2: ld returned 1 exit status
>> >> >> gmake[1]: *** [cmTryCompileExec2668319475] Error 1
>> >> >> gmake[1]: Leaving directory
>> >> >> `/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
>> >> >> gmake: *** [cmTryCompileExec2668319475/fast] Error 2
>> >> >>
>> >> >>
>> >> >> Kindly help. I tried installing 4.5.6 and it got installed without
>> >> any
>> >> >> such problems. I need 4.6 because my tpr files are produced in
>> >> >> Gromacs4.6
>> >> >> and I am using the Verlet cutoff scheme.
>> >>
>> >> Thank you Mark and Christoph for your replies. I solved the
>> installation
>> >> problem by configuring gromacs with static libraries. I somehow
>> didn't
>> >> notice earlier, there was a note saying that Shared Libraries might
>> be
>> >> problematic with MPI.
>> >>
>> >> With Regards
>> >> Abhishek
>> >> --
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