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

Mon Mar 4 23:42:38 CET 2013

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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