[gmx-users] MPICH or LAM/MPI
Carsten Kutzner
ckutzne at gwdg.de
Tue Jun 20 10:05:18 CEST 2006
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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/research/dep/grubmueller/
http://www.gwdg.de/~ckutzne
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