[gmx-users] problem in compiling GMX with MPI

Fri Sep 23 00:44:56 CEST 2011

On 23/09/2011 2:04 AM, Jinan Niu wrote:
>
>  Hi, Mark:
>
> Thanks for your reply.
> my configure line is just simple :
>
> ./configure --prefix=/home/njn/zms/1gmx4.5.5  --enable-mpi
>
> this would cause the  following error:
> ---------------------------------------------------------------------------------------------------
>
> ......
> checking size of off_t... configure: error: in 
> `/home/njn/Desktop/gromacs-4.5.5':
> configure: error: cannot compute sizeof (off_t)
> See `config.log' for more details.
>

Unfortunately it looks like your MPI compiler is not set up correctly. 
Can you compile other MPI programs with it?

Mark

> --------------------------------------------------------------------------------------------------
>
> In the  config.log, I found:
>
> ---------------------------------------------------------------------------------------------------------------------------------------------
>
> configure:4386: $? = 0
> configure:4375: cc -v >&5
> Using built-in specs.
> Target: x86_64-redhat-linux
> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man 
> --infodir=/usr/share/info 
> --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap 
> --enable-shared --enable-threads=posix --enable-checking=release 
> --with-system-zlib --enable-__cxa_atexit 
> --disable-libunwind-exceptions --enable-gnu-unique-object 
> --enable-languages=c,c++,objc,obj-c++,java,fortran,ada 
> --enable-java-awt=gtk --disable-dssi 
> --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre 
> --enable-libgcj-multifile --enable-java-maintainer-mode 
> --with-ecj-jar=/usr/share/java/eclipse-ecj.jar 
> --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic 
> --with-arch_32=i686 --build=x86_64-redhat-linux
> Thread model: posix
> gcc version 4.4.5 20110214 (Red Hat 4.4.5-6) (GCC)
> configure:4386: $? = 0
> configure:4375: cc -V >&5
> cc: '-V' option must have ar gument
> configure:4386: $? = 1
> configure:4375: cc -qversion >&5
> cc: unrecognized option '-qversion'
> cc: no input files
> configure:4386: $? = 1
> configure:4408: checking for C compiler default output file name
> configure:4430: cc    conftest.c >&5
> configure:4434: $? = 0
> configure:4471: result: a.out
> configure:4487: checking whether the C compiler works
> configure:4496: ./a.out
> configure:4500: $? = 0
> configure:4515: result: yes
> configure:4522: checking whether we are cross compiling
> configure:4524: result: no
> configure:4527: checking for suffix of executables
> configure:4534: cc -o conftest    conftest.c >&5
> configure:4538: $? = 0
> configure:4560: result:
> configure:4566: checking for suffix of object files
> configure:4588: cc -c   conftest.c >&5
> configure:4592: $? = 0
> configure:4613: result: o
> configure:4617: checking whether we are u sing the GNU C compiler
> configure:4636: cc -c   conftest.c >&5
> configure:4636: $? = 0
> configure:4645: result: yes
> configure:4654: checking whether cc accepts -g
> configure:4674: cc -c -g  conftest.c >&5
> configure:4674: $? = 0
> configure:4715: result: yes
> configure:4732: checking for cc option to accept ISO C89
> configure:4796: cc  -c -g -O2  conftest.c >&5
> configure:4796: $? = 0
> configure:4809: result: none needed
> configure:4840: checking for style of include used by make
> configure:4868: result: GNU
> configure:4893: checking dependency style of cc
> configure:5003: result: gcc3
> configure:5262: checking dependency style of cc
> configure:5370: result: gcc3
> configure:5396: checking for mpxlc
> configure:5426: result: no
> configure:5396: checking for mpicc
> configure:5412: found /usr/lib64/openmpi/bin/mpicc
> configure:5423: result: mpicc
> configure:5438: checking whether the MPI cc command works
> configure:5452: mpicc -o conftest -g -O2   conftest.c >&5
> configure:5452: $? = 0
> configure:5453: result: yes
> configure:5470: checking for MPI_IN_PLACE in collective operations
> configure:5490: mpicc -c -g -O2  conftest.c >&5
> configure:5490: $? = 0
> configure:5492: result: yes
> configure:5511: checking for catamount
> configure:5529: mpicc -c -g -O2  conftest.c >&5
> conftest.c:23:2: error: #error not catamount
> configure:5529: $? = 1
>
> configure: failed program was:
> | /* confdefs.h */
> | #define PACKAGE_NAME "gromacs"
> | #define PACKAGE_TARNAME "gromacs"
> | #define PACKAGE_VERSION "4.5.5"
> | #define PACKAGE_STRING "gromacs 4.5.5"
> | #define PACKAGE_BUGREPORT "gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>"
> | #define PACKAGE_URL ""
> | #define PACKAGE "gromacs"
> | #define VERSION "4.5.5"
> | #define GMX_SOFTWARE_INVSQRT /**/
> | #define GMX_QMMM_GAUSSIAN /**/
> | #define GMX_QMMM_ORCA /**/
> | #define BUILD_TIME "Thu Sep 22 23:33:40 CST 2011"
> | #define BUILD_USER "njn at njn-SL <mailto:njn at njn-SL>"
> | #define BUILD_MACHINE "Linux 2.6.32-131.0.15.el6.x86_64 x86_64"
> | #define GMX_MPI /**/
> | #define GMX_LIB_MPI /**/
> | #define MPI_IN_PLACE_EXISTS /**/
> | /* end confdefs.h.  */
> |
> | #if defined __QK_USER__
> | #else
> | #error not catamount
> | #endif
> |
> | int
> | main ()
> | {
> |
> |   ;
> |   retu rn 0;
> | }
> configure:5551: result: no
> configure:6229: checking how to run the C preprocessor
> configure:6260: mpicc -E  conftest.c
> configure:6260: $? = 0
> configure:6274: mpicc -E  conftest.c
> conftest.c:22:28: error: ac_nonexistent.h: No such file or directory
> configure:6274: $? = 1
> configure: failed program was:
> | /* confdefs.h */
> .......
> --------------------------------------------------------------------------------------------------------------------------------------------
> my system is scientific linux, kernel linux 2.6.32-131.0.15.el16.x86_64
> my gcc is 4.4.5
> my cpu is intel-i7-940 4 cores
>
> ?????????????????????????????????????????????????
>
> > More useful would be the information that you've been following the
> > online installation guide, and what your configure line was. As it is,
> > it looks like you have some problem with the compiler. Can you compile
> > other code?
> >
> > Mark
>
>
> --
> Sincerely yours
> Dr Ji-Nan Niu
> School of Materials Science and Engineering.
> China University of Mining and Technology.
> Jiangsu Province, XuZhou 221116
> P. R. China
>
>
>
>
>

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