[gmx-users] problem in compiling GMX with MPI

[Jinan Niu]

 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.

--------------------------------------------------------------------------------------------------

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 argument
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 using 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"
| #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"
| #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 ()
| {
|
|   ;
|   return 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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