[gmx-users] MPICH or LAM/MPI
Arneh Babakhani
ababakha at mccammon.ucsd.edu
Tue Jun 20 20:03:25 CEST 2006
Hi Carsten,
Yep, that was exactly it. When I included that path in my
LD_LIBRARY_PATH variable, it configured and compiled no problem.
Thanks!
Arneh
Carsten Kutzner wrote:
> Hi Arneh,
>
> the problem seems to me that the program that has to determine the
> size of an int cannot be compiled due to a missing LAM library:
>
> ---
> error while loading shared libraries: liblamf77mpi.so.0: cannot open
> shared object file: No such file or directory
> ---
>
> So make shure that this library can be found, probably in
> /path-to-lam-installation/lib
>
> Hope that helps,
> Carsten
>
>
> Arneh Babakhani wrote:
>> Hello, on this note, I'm having issues configuring and installing the
>> mpi enabled mdrun. (see below). I keep getting a strange error:
>> *checking size of int... configure: error: cannot compute sizeof
>> (int), 77
>> *I've pasted the output below, and I've attached the config.log for
>> reference. I'm really not sure what's going on here, so if anybody
>> could help, would greatly appreciate it.
>>
>> Regards,
>>
>> Arneh*
>> *
>> [ababakha at chemcca40 gromacs-3.3.1]$ ./configure --enable-mpi
>> --prefix=/home/ababakha/gromacs-mpi
>> checking build system type... i686-pc-linux-gnu
>> checking host system type... i686-pc-linux-gnu
>> checking for a BSD-compatible install... /usr/bin/install -c
>> checking whether build environment is sane... yes
>> checking for gawk... gawk
>> checking whether make sets $(MAKE)... yes
>> checking how to create a ustar tar archive... gnutar
>> checking for cc... cc
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether cc accepts -g... yes
>> checking for cc option to accept ANSI C... none needed
>> checking for style of include used by make... GNU
>> checking dependency style of cc... gcc3
>> checking for mpxlc... no
>> checking for mpicc... mpicc
>> checking whether the MPI cc command works... yes
>> checking how to run the C preprocessor... mpicc -E
>> checking whether mpicc accepts -O3... yes
>> checking whether mpicc accepts -malign-double... yes
>> checking whether mpicc accepts -funroll-all-loops... yes
>> checking whether mpicc accepts -O3 -fomit-frame-pointer
>> -finline-functions -Wall -Wno-unused -malign-double
>> -funroll-all-loops... yes
>> checking whether byte ordering is bigendian... no
>> checking for egrep... grep -E
>> checking for ANSI C header files... no
>> checking for sys/types.h... yes
>> checking for sys/stat.h... yes
>> checking for stdlib.h... yes
>> checking for string.h... yes
>> checking for memory.h... yes
>> checking for strings.h... yes
>> checking for inttypes.h... yes
>> checking for stdint.h... yes
>> checking for unistd.h... yes
>> checking for int... yes
>> checking size of int... configure: error: cannot compute sizeof
>> (int), 77
>> See `config.log' for more details.
>>
>>
>> ------------------------------------------------------------------------
>>
>> This file contains any messages produced by compilers while
>> running configure, to aid debugging if configure makes a mistake.
>>
>> It was created by GROMACS configure 3.3.1, which was
>> generated by GNU Autoconf 2.59. Invocation command line was
>>
>> $ ./configure --enable-mpi --prefix=/home/ababakha/bin/gromacs-mpi
>>
>> ## --------- ##
>> ## Platform. ##
>> ## --------- ##
>>
>> hostname = chemcca40.ucsd.edu
>> uname -m = i686
>> uname -r = 2.6.9-22.ELsmp
>> uname -s = Linux
>> uname -v = #1 SMP Sat Oct 8 19:11:43 CDT 2005
>>
>> /usr/bin/uname -p = unknown
>> /bin/uname -X = unknown
>>
>> /bin/arch = i686
>> /usr/bin/arch -k = unknown
>> /usr/convex/getsysinfo = unknown
>> hostinfo = unknown
>> /bin/machine = unknown
>> /usr/bin/oslevel = unknown
>> /bin/universe = unknown
>>
>> PATH: /home/ababakha/gromacs-3.3.1/bin
>> PATH: /home/ababakha/gromacs-3.3.1/bin
>> PATH: /opt/gridengine/bin/lx26-x86
>> PATH: /usr/kerberos/bin
>> PATH: /opt/intel/itc60/bin
>> PATH: /opt/intel/ita60/bin
>> PATH: /opt/intel/fc/9.0/bin
>> PATH: /opt/intel/idb/9.0/bin
>> PATH: /opt/intel/cc/9.0/bin
>> PATH: /usr/local/bin
>> PATH: /bin
>> PATH: /usr/bin
>> PATH: /opt/ganglia/bin
>> PATH: /opt/lam/gnu/bin
>> PATH: /usr/share/pvm3/lib
>> PATH: /usr/share/pvm3/lib/LINUX
>> PATH: /usr/share/pvm3/bin/LINUX
>> PATH: /opt/rocks/bin
>> PATH: /opt/rocks/sbin
>> PATH: /usr/X11R6/bin
>>
>>
>> ## ----------- ##
>> ## Core tests. ##
>> ## ----------- ##
>>
>> configure:1580: checking build system type
>> configure:1598: result: i686-pc-linux-gnu
>> configure:1606: checking host system type
>> configure:1620: result: i686-pc-linux-gnu
>> configure:1643: checking for a BSD-compatible install
>> configure:1698: result: /usr/bin/install -c
>> configure:1709: checking whether build environment is sane
>> configure:1752: result: yes
>> configure:1817: checking for gawk
>> configure:1833: found /bin/gawk
>> configure:1843: result: gawk
>> configure:1853: checking whether make sets $(MAKE)
>> configure:1873: result: yes
>> configure:2036: checking how to create a ustar tar archive
>> configure:2049: tar --version
>> tar (GNU tar) 1.14
>> Copyright (C) 2004 Free Software Foundation, Inc.
>> This program comes with NO WARRANTY, to the extent permitted by law.
>> You may redistribute it under the terms of the GNU General Public
>> License;
>> see the file named COPYING for details.
>> Written by John Gilmore and Jay Fenlason.
>> configure:2052: $? = 0
>> configure:2092: tardir=conftest.dir && eval tar --format=ustar -chf -
>> "$tardir" >conftest.tar
>> configure:2095: $? = 0
>> configure:2099: tar -xf - <conftest.tar
>> configure:2102: $? = 0
>> configure:2115: result: gnutar
>> configure:2663: checking for cc
>> configure:2679: found /usr/bin/cc
>> configure:2689: result: cc
>> configure:2710: checking for C compiler version
>> configure:2713: cc --version </dev/null >&5
>> cc (GCC) 3.4.4 20050721 (Red Hat 3.4.4-2)
>> Copyright (C) 2004 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:2716: $? = 0
>> configure:2718: cc -v </dev/null >&5
>> Reading specs from /usr/lib/gcc/i386-redhat-linux/3.4.4/specs
>> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
>> --infodir=/usr/share/info --enable-shared --enable-threads=posix
>> --disable-checking --with-system-zlib --enable-__cxa_atexit
>> --disable-libunwind-exceptions --enable-java-awt=gtk
>> --host=i386-redhat-linux
>> Thread model: posix
>> gcc version 3.4.4 20050721 (Red Hat 3.4.4-2)
>> configure:2721: $? = 0
>> configure:2723: cc -V </dev/null >&5
>> cc: `-V' option must have argument
>> configure:2726: $? = 1
>> configure:2749: checking for C compiler default output file name
>> configure:2752: cc -I/home/ababakha/fftw-3.0.1/include
>> -L/home/ababakha/fftw-3.0.1/lib conftest.c >&5
>> configure:2755: $? = 0
>> configure:2801: result: a.out
>> configure:2806: checking whether the C compiler works
>> configure:2812: ./a.out
>> configure:2815: $? = 0
>> configure:2832: result: yes
>> configure:2839: checking whether we are cross compiling
>> configure:2841: result: no
>> configure:2844: checking for suffix of executables
>> configure:2846: cc -o conftest -I/home/ababakha/fftw-3.0.1/include
>> -L/home/ababakha/fftw-3.0.1/lib conftest.c >&5
>> configure:2849: $? = 0
>> configure:2874: result: configure:2880: checking for suffix of object
>> files
>> configure:2901: cc -c -I/home/ababakha/fftw-3.0.1/include conftest.c
>> >&5
>> configure:2904: $? = 0
>> configure:2926: result: o
>> configure:2930: checking whether we are using the GNU C compiler
>> configure:2954: cc -c -I/home/ababakha/fftw-3.0.1/include conftest.c
>> >&5
>> configure:2960: $? = 0
>> configure:2964: test -z || test ! -s conftest.err
>> configure:2967: $? = 0
>> configure:2970: test -s conftest.o
>> configure:2973: $? = 0
>> configure:2986: result: yes
>> configure:2992: checking whether cc accepts -g
>> configure:3013: cc -c -g -I/home/ababakha/fftw-3.0.1/include
>> conftest.c >&5
>> configure:3019: $? = 0
>> configure:3023: test -z || test ! -s conftest.err
>> configure:3026: $? = 0
>> configure:3029: test -s conftest.o
>> configure:3032: $? = 0
>> configure:3043: result: yes
>> configure:3060: checking for cc option to accept ANSI C
>> configure:3130: cc -c -g -O2 -I/home/ababakha/fftw-3.0.1/include
>> conftest.c >&5
>> configure:3136: $? = 0
>> configure:3140: test -z || test ! -s conftest.err
>> configure:3143: $? = 0
>> configure:3146: test -s conftest.o
>> configure:3149: $? = 0
>> configure:3167: result: none needed
>> configure:3185: cc -c -g -O2 -I/home/ababakha/fftw-3.0.1/include
>> conftest.c >&5
>> conftest.c:2: error: syntax error before "me"
>> configure:3191: $? = 1
>> configure: failed program was:
>> | #ifndef __cplusplus
>> | choke me
>> | #endif
>> configure:3335: checking for style of include used by make
>> configure:3363: result: GNU
>> configure:3391: checking dependency style of cc
>> configure:3481: result: gcc3
>> configure:3757: checking for mpxlc
>> configure:3786: result: no
>> configure:3757: checking for mpicc
>> configure:3773: found /opt/lam/gnu/bin/mpicc
>> configure:3783: result: mpicc
>> configure:3796: checking whether the MPI cc command works
>> configure:3815: mpicc -o conftest -g -O2
>> -I/home/ababakha/fftw-3.0.1/include -L/home/ababakha/fftw-3.0.1/lib
>> conftest.c >&5
>> configure:3821: $? = 0
>> configure:3825: test -z || test ! -s conftest.err
>> configure:3828: $? = 0
>> configure:3831: test -s conftest
>> configure:3834: $? = 0
>> configure:3836: result: yes
>> configure:4720: checking how to run the C preprocessor
>> configure:4755: mpicc -E -I/home/ababakha/fftw-3.0.1/include conftest.c
>> configure:4761: $? = 0
>> configure:4793: mpicc -E -I/home/ababakha/fftw-3.0.1/include conftest.c
>> conftest.c:19:28: ac_nonexistent.h: No such file or directory
>> mpicc: No such file or directory
>> configure:4799: $? = 1
>> configure: failed program was:
>> | /* confdefs.h. */
>> | | #define PACKAGE_NAME "GROMACS"
>> | #define PACKAGE_TARNAME "gromacs"
>> | #define PACKAGE_VERSION "3.3.1"
>> | #define PACKAGE_STRING "GROMACS 3.3.1"
>> | #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
>> | #define PACKAGE "gromacs"
>> | #define VERSION "3.3.1"
>> | #define GMX_SOFTWARE_SQRT
>> | #define GMX_QMMM_GAUSSIAN
>> | #define BUILD_TIME "Fri Jun 16 15:17:11 PDT 2006"
>> | #define BUILD_USER "ababakha at chemcca40.ucsd.edu"
>> | #define BUILD_MACHINE "Linux 2.6.9-22.ELsmp i686"
>> | #define GMX_MPI
>> | #define F77_OR_C_FUNC(name,NAME) name
>> | #define F77_OR_C_FUNC_(name,NAME) name
>> | /* end confdefs.h. */
>> | #include <ac_nonexistent.h>
>> configure:4838: result: mpicc -E
>> configure:4862: mpicc -E -I/home/ababakha/fftw-3.0.1/include conftest.c
>> configure:4868: $? = 0
>> configure:4900: mpicc -E -I/home/ababakha/fftw-3.0.1/include conftest.c
>> conftest.c:19:28: ac_nonexistent.h: No such file or directory
>> mpicc: No such file or directory
>> configure:4906: $? = 1
>> configure: failed program was:
>> | /* confdefs.h. */
>> | | #define PACKAGE_NAME "GROMACS"
>> | #define PACKAGE_TARNAME "gromacs"
>> | #define PACKAGE_VERSION "3.3.1"
>> | #define PACKAGE_STRING "GROMACS 3.3.1"
>> | #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
>> | #define PACKAGE "gromacs"
>> | #define VERSION "3.3.1"
>> | #define GMX_SOFTWARE_SQRT
>> | #define GMX_QMMM_GAUSSIAN
>> | #define BUILD_TIME "Fri Jun 16 15:17:11 PDT 2006"
>> | #define BUILD_USER "ababakha at chemcca40.ucsd.edu"
>> | #define BUILD_MACHINE "Linux 2.6.9-22.ELsmp i686"
>> | #define GMX_MPI
>> | #define F77_OR_C_FUNC(name,NAME) name
>> | #define F77_OR_C_FUNC_(name,NAME) name
>> | /* end confdefs.h. */
>> | #include <ac_nonexistent.h>
>> configure:5337: checking whether mpicc accepts -O3
>> configure:5355: result: yes
>> configure:5379: checking whether mpicc accepts -malign-double
>> configure:5397: result: yes
>> configure:5666: checking whether mpicc accepts -funroll-all-loops
>> configure:5684: result: yes
>> configure:5723: checking whether mpicc accepts -O3
>> -fomit-frame-pointer -finline-functions -Wall -Wno-unused
>> -malign-double -funroll-all-loops
>> configure:5741: result: yes
>> configure:5832: checking whether byte ordering is bigendian
>> configure:5867: mpicc -c -O3 -fomit-frame-pointer -finline-functions
>> -Wall -Wno-unused -malign-double -funroll-all-loops
>> -I/home/ababakha/fftw-3.0.1/include conftest.c >&5
>> configure:5873: $? = 0
>> configure:5877: test -z || test ! -s conftest.err
>> configure:5880: $? = 0
>> configure:5883: test -s conftest.o
>> configure:5886: $? = 0
>> configure:5918: mpicc -c -O3 -fomit-frame-pointer -finline-functions
>> -Wall -Wno-unused -malign-double -funroll-all-loops
>> -I/home/ababakha/fftw-3.0.1/include conftest.c >&5
>> conftest.c: In function `main':
>> conftest.c:34: error: `not' undeclared (first use in this function)
>> conftest.c:34: error: (Each undeclared identifier is reported only once
>> conftest.c:34: error: for each function it appears in.)
>> conftest.c:34: error: syntax error before "big"
>> mpicc: No such file or directory
>> configure:5924: $? = 1
>> configure: failed program was:
>> | /* confdefs.h. */
>> | | #define PACKAGE_NAME "GROMACS"
>> | #define PACKAGE_TARNAME "gromacs"
>> | #define PACKAGE_VERSION "3.3.1"
>> | #define PACKAGE_STRING "GROMACS 3.3.1"
>> | #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
>> | #define PACKAGE "gromacs"
>> | #define VERSION "3.3.1"
>> | #define GMX_SOFTWARE_SQRT
>> | #define GMX_QMMM_GAUSSIAN
>> | #define BUILD_TIME "Fri Jun 16 15:17:11 PDT 2006"
>> | #define BUILD_USER "ababakha at chemcca40.ucsd.edu"
>> | #define BUILD_MACHINE "Linux 2.6.9-22.ELsmp i686"
>> | #define GMX_MPI
>> | #define F77_OR_C_FUNC(name,NAME) name
>> | #define F77_OR_C_FUNC_(name,NAME) name
>> | /* end confdefs.h. */
>> | #include <sys/types.h>
>> | #include <sys/param.h>
>> | | #ifdef F77_DUMMY_MAIN
>> | | # ifdef __cplusplus
>> | extern "C"
>> | # endif
>> | int F77_DUMMY_MAIN() { return 1; }
>> | | #endif
>> | int
>> | main ()
>> | {
>> | #if BYTE_ORDER != BIG_ENDIAN
>> | not big endian
>> | #endif
>> | | ;
>> | return 0;
>> | }
>> configure:6067: result: no
>> configure:6091: checking for egrep
>> configure:6101: result: grep -E
>> configure:6106: checking for ANSI C header files
>> configure:6139: mpicc -c -O3 -fomit-frame-pointer -finline-functions
>> -Wall -Wno-unused -malign-double -funroll-all-loops
>> -I/home/ababakha/fftw-3.0.1/include conftest.c >&5
>> configure:6145: $? = 0
>> configure:6149: test -z || test ! -s conftest.err
>> configure:6152: $? = 0
>> configure:6155: test -s conftest.o
>> configure:6158: $? = 0
>> configure:6247: mpicc -o conftest -O3 -fomit-frame-pointer
>> -finline-functions -Wall -Wno-unused -malign-double
>> -funroll-all-loops -I/home/ababakha/fftw-3.0.1/include
>> -L/home/ababakha/fftw-3.0.1/lib conftest.c >&5
>> conftest.c: In function `main':
>> conftest.c:36: warning: implicit declaration of function `exit'
>> configure:6250: $? = 0
>> configure:6252: ./conftest
>> ./conftest: error while loading shared libraries: liblamf77mpi.so.0:
>> cannot open shared object file: No such file or directory
>> configure:6255: $? = 127
>> configure: program exited with status 127
>> configure: failed program was:
>> | /* confdefs.h. */
>> | | #define PACKAGE_NAME "GROMACS"
>> | #define PACKAGE_TARNAME "gromacs"
>> | #define PACKAGE_VERSION "3.3.1"
>> | #define PACKAGE_STRING "GROMACS 3.3.1"
>> | #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
>> | #define PACKAGE "gromacs"
>> | #define VERSION "3.3.1"
>> | #define GMX_SOFTWARE_SQRT
>> | #define GMX_QMMM_GAUSSIAN
>> | #define BUILD_TIME "Fri Jun 16 15:17:11 PDT 2006"
>> | #define BUILD_USER "ababakha at chemcca40.ucsd.edu"
>> | #define BUILD_MACHINE "Linux 2.6.9-22.ELsmp i686"
>> | #define GMX_MPI
>> | #define F77_OR_C_FUNC(name,NAME) name
>> | #define F77_OR_C_FUNC_(name,NAME) name
>> | /* end confdefs.h. */
>> | #include <ctype.h>
>> | #if ((' ' & 0x0FF) == 0x020)
>> | # define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
>> | # define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
>> | #else
>> | # define ISLOWER(c) (('a' <= (c) && (c) <=
>> 'i') || ('j' <= (c) && (c) <= 'r') || ('s'
>> <= (c) && (c) <= 'z'))
>> | # define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c))
>> | #endif
>> | | #define XOR(e, f) (((e) && !(f)) || (!(e) && (f)))
>> | int
>> | main ()
>> | {
>> | int i;
>> | for (i = 0; i < 256; i++)
>> | if (XOR (islower (i), ISLOWER (i))
>> | || toupper (i) != TOUPPER (i))
>> | exit(2);
>> | exit (0);
>> | }
>> configure:6270: result: no
>> configure:6294: checking for sys/types.h
>> configure:6310: mpicc -c -O3 -fomit-frame-pointer -finline-functions
>> -Wall -Wno-unused -malign-double -funroll-all-loops
>> -I/home/ababakha/fftw-3.0.1/include conftest.c >&5
>> configure:6316: $? = 0
>> configure:6320: test -z || test ! -s conftest.err
>> configure:6323: $? = 0
>> configure:6326: test -s conftest.o
>> configure:6329: $? = 0
>> configure:6340: result: yes
>> configure:6294: checking for sys/stat.h
>> configure:6310: mpicc -c -O3 -fomit-frame-pointer -finline-functions
>> -Wall -Wno-unused -malign-double -funroll-all-loops
>> -I/home/ababakha/fftw-3.0.1/include conftest.c >&5
>> configure:6316: $? = 0
>> configure:6320: test -z || test ! -s conftest.err
>> configure:6323: $? = 0
>> configure:6326: test -s conftest.o
>> configure:6329: $? = 0
>> configure:6340: result: yes
>> configure:6294: checking for stdlib.h
>> configure:6310: mpicc -c -O3 -fomit-frame-pointer -finline-functions
>> -Wall -Wno-unused -malign-double -funroll-all-loops
>> -I/home/ababakha/fftw-3.0.1/include conftest.c >&5
>> configure:6316: $? = 0
>> configure:6320: test -z || test ! -s conftest.err
>> configure:6323: $? = 0
>> configure:6326: test -s conftest.o
>> configure:6329: $? = 0
>> configure:6340: result: yes
>> configure:6294: checking for string.h
>> configure:6310: mpicc -c -O3 -fomit-frame-pointer -finline-functions
>> -Wall -Wno-unused -malign-double -funroll-all-loops
>> -I/home/ababakha/fftw-3.0.1/include conftest.c >&5
>> configure:6316: $? = 0
>> configure:6320: test -z || test ! -s conftest.err
>> configure:6323: $? = 0
>> configure:6326: test -s conftest.o
>> configure:6329: $? = 0
>> configure:6340: result: yes
>> configure:6294: checking for memory.h
>> configure:6310: mpicc -c -O3 -fomit-frame-pointer -finline-functions
>> -Wall -Wno-unused -malign-double -funroll-all-loops
>> -I/home/ababakha/fftw-3.0.1/include conftest.c >&5
>> configure:6316: $? = 0
>> configure:6320: test -z || test ! -s conftest.err
>> configure:6323: $? = 0
>> configure:6326: test -s conftest.o
>> configure:6329: $? = 0
>> configure:6340: result: yes
>> configure:6294: checking for strings.h
>> configure:6310: mpicc -c -O3 -fomit-frame-pointer -finline-functions
>> -Wall -Wno-unused -malign-double -funroll-all-loops
>> -I/home/ababakha/fftw-3.0.1/include conftest.c >&5
>> configure:6316: $? = 0
>> configure:6320: test -z || test ! -s conftest.err
>> configure:6323: $? = 0
>> configure:6326: test -s conftest.o
>> configure:6329: $? = 0
>> configure:6340: result: yes
>> configure:6294: checking for inttypes.h
>> configure:6310: mpicc -c -O3 -fomit-frame-pointer -finline-functions
>> -Wall -Wno-unused -malign-double -funroll-all-loops
>> -I/home/ababakha/fftw-3.0.1/include conftest.c >&5
>> configure:6316: $? = 0
>> configure:6320: test -z || test ! -s conftest.err
>> configure:6323: $? = 0
>> configure:6326: test -s conftest.o
>> configure:6329: $? = 0
>> configure:6340: result: yes
>> configure:6294: checking for stdint.h
>> configure:6310: mpicc -c -O3 -fomit-frame-pointer -finline-functions
>> -Wall -Wno-unused -malign-double -funroll-all-loops
>> -I/home/ababakha/fftw-3.0.1/include conftest.c >&5
>> configure:6316: $? = 0
>> configure:6320: test -z || test ! -s conftest.err
>> configure:6323: $? = 0
>> configure:6326: test -s conftest.o
>> configure:6329: $? = 0
>> configure:6340: result: yes
>> configure:6294: checking for unistd.h
>> configure:6310: mpicc -c -O3 -fomit-frame-pointer -finline-functions
>> -Wall -Wno-unused -malign-double -funroll-all-loops
>> -I/home/ababakha/fftw-3.0.1/include conftest.c >&5
>> configure:6316: $? = 0
>> configure:6320: test -z || test ! -s conftest.err
>> configure:6323: $? = 0
>> configure:6326: test -s conftest.o
>> configure:6329: $? = 0
>> configure:6340: result: yes
>> configure:6352: checking for int
>> configure:6384: mpicc -c -O3 -fomit-frame-pointer -finline-functions
>> -Wall -Wno-unused -malign-double -funroll-all-loops
>> -I/home/ababakha/fftw-3.0.1/include conftest.c >&5
>> configure:6390: $? = 0
>> configure:6394: test -z || test ! -s conftest.err
>> configure:6397: $? = 0
>> configure:6400: test -s conftest.o
>> configure:6403: $? = 0
>> configure:6414: result: yes
>> configure:6417: checking size of int
>> configure:6784: mpicc -o conftest -O3 -fomit-frame-pointer
>> -finline-functions -Wall -Wno-unused -malign-double
>> -funroll-all-loops -I/home/ababakha/fftw-3.0.1/include
>> -L/home/ababakha/fftw-3.0.1/lib conftest.c >&5
>> configure:6787: $? = 0
>> configure:6789: ./conftest
>> ./conftest: error while loading shared libraries: liblamf77mpi.so.0:
>> cannot open shared object file: No such file or directory
>> configure:6792: $? = 127
>> configure: program exited with status 127
>> configure: failed program was:
>> | /* confdefs.h. */
>> | | #define PACKAGE_NAME "GROMACS"
>> | #define PACKAGE_TARNAME "gromacs"
>> | #define PACKAGE_VERSION "3.3.1"
>> | #define PACKAGE_STRING "GROMACS 3.3.1"
>> | #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
>> | #define PACKAGE "gromacs"
>> | #define VERSION "3.3.1"
>> | #define GMX_SOFTWARE_SQRT
>> | #define GMX_QMMM_GAUSSIAN
>> | #define BUILD_TIME "Fri Jun 16 15:17:11 PDT 2006"
>> | #define BUILD_USER "ababakha at chemcca40.ucsd.edu"
>> | #define BUILD_MACHINE "Linux 2.6.9-22.ELsmp i686"
>> | #define GMX_MPI
>> | #define F77_OR_C_FUNC(name,NAME) name
>> | #define F77_OR_C_FUNC_(name,NAME) name
>> | #define HAVE_SYS_TYPES_H 1
>> | #define HAVE_SYS_STAT_H 1
>> | #define HAVE_STDLIB_H 1
>> | #define HAVE_STRING_H 1
>> | #define HAVE_MEMORY_H 1
>> | #define HAVE_STRINGS_H 1
>> | #define HAVE_INTTYPES_H 1
>> | #define HAVE_STDINT_H 1
>> | #define HAVE_UNISTD_H 1
>> | /* end confdefs.h. */
>> | #include <stdio.h>
>> | #if HAVE_SYS_TYPES_H
>> | # include <sys/types.h>
>> | #endif
>> | #if HAVE_SYS_STAT_H
>> | # include <sys/stat.h>
>> | #endif
>> | #if STDC_HEADERS
>> | # include <stdlib.h>
>> | # include <stddef.h>
>> | #else
>> | # if HAVE_STDLIB_H
>> | # include <stdlib.h>
>> | # endif
>> | #endif
>> | #if HAVE_STRING_H
>> | # if !STDC_HEADERS && HAVE_MEMORY_H
>> | # include <memory.h>
>> | # endif
>> | # include <string.h>
>> | #endif
>> | #if HAVE_STRINGS_H
>> | # include <strings.h>
>> | #endif
>> | #if HAVE_INTTYPES_H
>> | # include <inttypes.h>
>> | #else
>> | # if HAVE_STDINT_H
>> | # include <stdint.h>
>> | # endif
>> | #endif
>> | #if HAVE_UNISTD_H
>> | # include <unistd.h>
>> | #endif
>> | long longval () { return (long) (sizeof (int)); }
>> | unsigned long ulongval () { return (long) (sizeof (int)); }
>> | #include <stdio.h>
>> | #include <stdlib.h>
>> | #ifdef F77_DUMMY_MAIN
>> | | # ifdef __cplusplus
>> | extern "C"
>> | # endif
>> | int F77_DUMMY_MAIN() { return 1; }
>> | | #endif
>> | int
>> | main ()
>> | {
>> | | FILE *f = fopen ("conftest.val", "w");
>> | if (! f)
>> | exit (1);
>> | if (((long) (sizeof (int))) < 0)
>> | {
>> | long i = longval ();
>> | if (i != ((long) (sizeof (int))))
>> | exit (1);
>> | fprintf (f, "%ld\n", i);
>> | }
>> | else
>> | {
>> | unsigned long i = ulongval ();
>> | if (i != ((long) (sizeof (int))))
>> | exit (1);
>> | fprintf (f, "%lu\n", i);
>> | }
>> | exit (ferror (f) || fclose (f) != 0);
>> | | ;
>> | return 0;
>> | }
>> configure:6802: error: cannot compute sizeof (int), 77
>> See `config.log' for more details.
>>
>> ## ---------------- ##
>> ## Cache variables. ##
>> ## ---------------- ##
>>
>> ac_cv_build=i686-pc-linux-gnu
>> ac_cv_build_alias=i686-pc-linux-gnu
>> ac_cv_c_bigendian=no
>> ac_cv_c_compiler_gnu=yes
>> ac_cv_env_CC_set=
>> ac_cv_env_CC_value=
>> ac_cv_env_CFLAGS_set=
>> ac_cv_env_CFLAGS_value=
>> ac_cv_env_CPPFLAGS_set=set
>> ac_cv_env_CPPFLAGS_value=-I/home/ababakha/fftw-3.0.1/include
>> ac_cv_env_CPP_set=
>> ac_cv_env_CPP_value=
>> ac_cv_env_CXXCPP_set=
>> ac_cv_env_CXXCPP_value=
>> ac_cv_env_CXXFLAGS_set=
>> ac_cv_env_CXXFLAGS_value=
>> ac_cv_env_CXX_set=
>> ac_cv_env_CXX_value=
>> ac_cv_env_F77_set=
>> ac_cv_env_F77_value=
>> ac_cv_env_FFLAGS_set=
>> ac_cv_env_FFLAGS_value=
>> ac_cv_env_LDFLAGS_set=set
>> ac_cv_env_LDFLAGS_value=-L/home/ababakha/fftw-3.0.1/lib
>> ac_cv_env_build_alias_set=
>> ac_cv_env_build_alias_value=
>> ac_cv_env_host_alias_set=
>> ac_cv_env_host_alias_value=
>> ac_cv_env_target_alias_set=
>> ac_cv_env_target_alias_value=
>> ac_cv_exeext=
>> ac_cv_header_inttypes_h=yes
>> ac_cv_header_memory_h=yes
>> ac_cv_header_stdc=no
>> ac_cv_header_stdint_h=yes
>> ac_cv_header_stdlib_h=yes
>> ac_cv_header_string_h=yes
>> ac_cv_header_strings_h=yes
>> ac_cv_header_sys_stat_h=yes
>> ac_cv_header_sys_types_h=yes
>> ac_cv_header_unistd_h=yes
>> ac_cv_host=i686-pc-linux-gnu
>> ac_cv_host_alias=i686-pc-linux-gnu
>> ac_cv_objext=o
>> ac_cv_path_install='/usr/bin/install -c'
>> ac_cv_prog_AWK=gawk
>> ac_cv_prog_CPP='mpicc -E'
>> ac_cv_prog_MPICC=mpicc
>> ac_cv_prog_ac_ct_CC=cc
>> ac_cv_prog_cc_g=yes
>> ac_cv_prog_cc_stdc=
>> ac_cv_prog_egrep='grep -E'
>> ac_cv_prog_make_make_set=yes
>> ac_cv_type_int=yes
>> am_cv_CC_dependencies_compiler_type=gcc3
>> am_cv_prog_tar_ustar=gnutar
>>
>> ## ----------------- ##
>> ## Output variables. ##
>> ## ----------------- ##
>>
>> ACLOCAL='${SHELL}
>> /home/ababakha/Downloads/gromacs-3.3.1/config/missing --run aclocal-1.9'
>> AMDEPBACKSLASH='\'
>> AMDEP_FALSE='#'
>> AMDEP_TRUE=''
>> AMTAR='${SHELL} /home/ababakha/Downloads/gromacs-3.3.1/config/missing
>> --run tar'
>> AR=''
>> AS=''
>> ASFLAGS=' -O3 -fomit-frame-pointer -finline-functions -Wall
>> -Wno-unused -malign-double -funroll-all-loops'
>> AUTOCONF='${SHELL}
>> /home/ababakha/Downloads/gromacs-3.3.1/config/missing --run autoconf'
>> AUTOHEADER='${SHELL}
>> /home/ababakha/Downloads/gromacs-3.3.1/config/missing --run autoheader'
>> AUTOMAKE='${SHELL}
>> /home/ababakha/Downloads/gromacs-3.3.1/config/missing --run
>> automake-1.9'
>> AWK='gawk'
>> CC='mpicc'
>> CCAS=''
>> CCASFLAGS=''
>> CCDEPMODE='depmode=gcc3'
>> CC_FOR_BUILD='cc'
>> CFLAGS=' -O3 -fomit-frame-pointer -finline-functions -Wall
>> -Wno-unused -malign-double -funroll-all-loops'
>> CPP='mpicc -E'
>> CPPFLAGS='-I/home/ababakha/fftw-3.0.1/include'
>> CXX=''
>> CXXCPP=''
>> CXXDEPMODE=''
>> CXXFLAGS=''
>> CYGPATH_W='echo'
>> DEFS=''
>> DEPDIR='.deps'
>> DLLTOOL=''
>> ECHO='echo'
>> ECHO_C=''
>> ECHO_N='-n'
>> ECHO_T=''
>> EGREP='grep -E'
>> EXEEXT=''
>> F77=''
>> F77LINK='$(LINK)'
>> FFLAGS=''
>> FLIBS=''
>> GMXANA_LIBOBJS=''
>> GMXLIB_LIBOBJS=''
>> GMX_DOUBLE_FALSE=''
>> GMX_DOUBLE_TRUE='#'
>> GMX_EXTERNAL_BLAS_FALSE=''
>> GMX_EXTERNAL_BLAS_TRUE='#'
>> GMX_EXTERNAL_LAPACK_FALSE=''
>> GMX_EXTERNAL_LAPACK_TRUE='#'
>> GMX_FORTRAN_FALSE=''
>> GMX_FORTRAN_TRUE='#'
>> GMX_IA32_3DNOW_FALSE=''
>> GMX_IA32_3DNOW_TRUE=''
>> GMX_IA32_SSE2_FALSE=''
>> GMX_IA32_SSE2_TRUE=''
>> GMX_IA32_SSE_FALSE=''
>> GMX_IA32_SSE_TRUE=''
>> GMX_IA64_ASM_DOUBLE_FALSE=''
>> GMX_IA64_ASM_DOUBLE_TRUE=''
>> GMX_IA64_ASM_SINGLE_FALSE=''
>> GMX_IA64_ASM_SINGLE_TRUE=''
>> GMX_PPC_ALTIVEC_FALSE=''
>> GMX_PPC_ALTIVEC_TRUE=''
>> GMX_PREFETCH_FORCES_FALSE=''
>> GMX_PREFETCH_FORCES_TRUE='#'
>> GMX_SOFTWARE_SQRT_FALSE='#'
>> GMX_SOFTWARE_SQRT_TRUE=''
>> GMX_THREAD_FALSE=''
>> GMX_THREAD_TRUE='#'
>> GMX_X86_64_SSE2_FALSE=''
>> GMX_X86_64_SSE2_TRUE=''
>> GMX_X86_64_SSE_FALSE=''
>> GMX_X86_64_SSE_TRUE=''
>> INCLUDES=''
>> INSTALL_DATA='${INSTALL} -m 644'
>> INSTALL_PROGRAM='${INSTALL}'
>> INSTALL_SCRIPT='${INSTALL}'
>> INSTALL_STRIP_PROGRAM='${SHELL} $(install_sh) -c -s'
>> LDFLAGS='-L/home/ababakha/fftw-3.0.1/lib '
>> LIBOBJS=''
>> LIBS=''
>> LIBSUFFIX=''
>> LIBTOOL=''
>> LN_S=''
>> LTLIBOBJS=''
>> MAKEINFO='${SHELL}
>> /home/ababakha/Downloads/gromacs-3.3.1/config/missing --run makeinfo'
>> MDLIB_LIBOBJS=' qm_gaussian.lo'
>> MPICC='mpicc'
>> OBJDUMP=''
>> OBJEXT='o'
>> PACKAGE='gromacs'
>> PACKAGE_BUGREPORT='gmx-users at gromacs.org'
>> PACKAGE_NAME='GROMACS'
>> PACKAGE_STRING='GROMACS 3.3.1'
>> PACKAGE_TARNAME='gromacs'
>> PACKAGE_VERSION='3.3.1'
>> PATH_SEPARATOR=':'
>> RANLIB=''
>> RPM=''
>> SET_MAKE=''
>> SHARED_VERSION_INFO='4:0:0'
>> SHELL='/bin/sh'
>> STRIP=''
>> USE_X11_FALSE=''
>> USE_X11_TRUE=''
>> VERSION='3.3.1'
>> X_CFLAGS=''
>> X_EXTRA_LIBS=''
>> X_LIBS=''
>> X_PRE_LIBS=''
>> ac_ct_AR=''
>> ac_ct_AS=''
>> ac_ct_CC='cc'
>> ac_ct_CXX=''
>> ac_ct_DLLTOOL=''
>> ac_ct_F77=''
>> ac_ct_OBJDUMP=''
>> ac_ct_RANLIB=''
>> ac_ct_STRIP=''
>> am__fastdepCC_FALSE='#'
>> am__fastdepCC_TRUE=''
>> am__fastdepCXX_FALSE=''
>> am__fastdepCXX_TRUE=''
>> am__include='include'
>> am__leading_dot='.'
>> am__quote=''
>> am__tar='tar --format=ustar -chf - "$$tardir"'
>> am__untar='tar -xf -'
>> bindir='${exec_prefix}/bin'
>> build='i686-pc-linux-gnu'
>> build_alias=''
>> build_cpu='i686'
>> build_os='linux-gnu'
>> build_vendor='pc'
>> datadir='${prefix}/share'
>> exec_prefix='NONE'
>> host='i686-pc-linux-gnu'
>> host_alias=''
>> host_cpu='i686'
>> host_os='linux-gnu'
>> host_vendor='pc'
>> includedir='${prefix}/include'
>> infodir='${prefix}/info'
>> install_sh='/home/ababakha/Downloads/gromacs-3.3.1/config/install-sh'
>> libdir='${exec_prefix}/lib'
>> libexecdir='${exec_prefix}/libexec'
>> localstatedir='${prefix}/var'
>> mandir='${prefix}/man'
>> mkdir_p='mkdir -p --'
>> oldincludedir='/usr/include'
>> prefix='/home/ababakha/bin/gromacs-mpi'
>> program_transform_name='s,x,x,'
>> sbindir='${exec_prefix}/sbin'
>> sharedstatedir='${prefix}/com'
>> sysconfdir='${prefix}/etc'
>> target_alias=''
>>
>> ## ----------- ##
>> ## confdefs.h. ##
>> ## ----------- ##
>>
>> #define BUILD_MACHINE "Linux 2.6.9-22.ELsmp i686"
>> #define BUILD_TIME "Fri Jun 16 15:17:11 PDT 2006"
>> #define BUILD_USER "ababakha at chemcca40.ucsd.edu"
>> #define F77_OR_C_FUNC(name,NAME) name
>> #define F77_OR_C_FUNC_(name,NAME) name
>> #define GMX_MPI
>> #define GMX_QMMM_GAUSSIAN
>> #define GMX_SOFTWARE_SQRT
>> #define HAVE_INTTYPES_H 1
>> #define HAVE_MEMORY_H 1
>> #define HAVE_STDINT_H 1
>> #define HAVE_STDLIB_H 1
>> #define HAVE_STRINGS_H 1
>> #define HAVE_STRING_H 1
>> #define HAVE_SYS_STAT_H 1
>> #define HAVE_SYS_TYPES_H 1
>> #define HAVE_UNISTD_H 1
>> #define PACKAGE "gromacs"
>> #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
>> #define PACKAGE_NAME "GROMACS"
>> #define PACKAGE_STRING "GROMACS 3.3.1"
>> #define PACKAGE_TARNAME "gromacs"
>> #define PACKAGE_VERSION "3.3.1"
>> #define VERSION "3.3.1"
>>
>> configure: exit 1
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
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>
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