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

[Abhishek Acharya]

> 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
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>