subject:"\[gmx\-users\] problem in compiling GMX with MPI"

Re: [gmx-users] problem in compiling GMX with MPI

2011-09-23 Thread Jinan Niu

thanks you,Mark
the problem has been solved.
I redefined the flag of openmpi, then gmx compliled successfully.




--

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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Re: [gmx-users] problem in compiling GMX with MPI

2011-09-22 Thread Mark Abraham


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: ccconftest.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 conftestconftest.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@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@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: $

Re: [gmx-users] problem in compiling GMX with MPI

2011-09-22 Thread 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: ccconftest.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 conftestconftest.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@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@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 */
...
--

Re: [gmx-users] problem in compiling GMX with MPI

2011-09-21 Thread Mark Abraham


On 21/09/2011 7:59 PM, Jinan Niu wrote:


Hi, everyone:
when I compiled GMX4.5.5, I encountered a problem and failed many 
times, SOS!

Below is my config.log:


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

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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[gmx-users] problem in compiling GMX with MPI

2011-09-21 Thread Jinan Niu



Hi, everyone:
when I compiled GMX4.5.5, I encountered a problem and failed many times， SOS!

Below is my config.log:

/usr/bin/uname -p = unknown
/bin/uname -X = unknown

/bin/arch  = x86_64
/usr/bin/arch -k   = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo  = unknown
/bin/machine   = unknown
/usr/bin/oslevel   = unknown
/bin/universe  = unknown

PATH: /usr/lib64/qt-3.3/bin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/local/sbin
PATH: /usr/sbin
PATH: /sbin
PATH: /usr/local/grace/bin
PATH: /usr/lib64/openmpi/bin
PATH: /home/njn/bin


## --- ##
## Core tests. ##
## --- ##

configure:3028: checking build system type
configure:3042: result: x86_64-unknown-linux-gnu
configure:3062: checking host system type
configure:3075: result: x86_64-unknown-linux-gnu
configure:3112: checking for a BSD-compatible install
configure:3180: result: /usr/bin/install -c
configure:3191: checking whether build environment is sane
configure:3241: result: yes
configure:3382: checking for a thread-safe mkdir -p
configure:3421: result: /bin/mkdir -p
configure:3434: checking for gawk
configure:3450: found /usr/bin/gawk
configure:3461: result: gawk
configure:3472: checking whether make sets $(MAKE)
configure:3494: result: yes
configure:3569: checking how to create a ustar tar archive
configure:3582: tar --version
tar (GNU tar) 1.23
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later .
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
configure:3585: $? = 0
configure:3625: tardir=conftest.dir && eval tar --format=ustar -chf - "$tardir" 
>conftest.tar
configure:3628: $? = 0
configure:3632: tar -xf - &5
cc (GCC) 4.4.5 20110214 (Red Hat 4.4.5-6)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

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: ccconftest.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 conftestconftest.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:6229: checking how to run the C preprocessor
configure:6260: cc -E  conftest.c
configure:6260: $? = 0

configure:6274: cc -E  conftest.c
conftest.c:19:28: error: ac_nonexistent.h: No such file or directory
configure:6274: $? = 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"

Re: [gmx-users] problem in compiling GMX with MPI

Re: [gmx-users] problem in compiling GMX with MPI

Re: [gmx-users] problem in compiling GMX with MPI

Re: [gmx-users] problem in compiling GMX with MPI

[gmx-users] problem in compiling GMX with MPI

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