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On 23/09/2011 2:04 AM, Jinan Niu wrote:
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cite="mid:f8d74d.145d4.13291e1c1b3.Coremail.njn0516@163.com"
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<p> Hi, Mark:</p>
<p>Thanks for your reply.<br>
my configure line is just simple :</p>
<p>./configure --prefix=/home/njn/zms/1gmx4.5.5 --enable-mpi</p>
<p>this would cause the following error:<br>
---------------------------------------------------------------------------------------------------</p>
<p>......<br>
checking size of off_t... configure: error: in
`/home/njn/Desktop/gromacs-4.5.5':<br>
configure: error: cannot compute sizeof (off_t)<br>
See `config.log' for more details.</p>
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<br>
Unfortunately it looks like your MPI compiler is not set up
correctly. Can you compile other MPI programs with it?<br>
<br>
Mark<br>
<br>
<blockquote
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<p>--------------------------------------------------------------------------------------------------</p>
<p>In the config.log, I found:</p>
<p>---------------------------------------------------------------------------------------------------------------------------------------------</p>
<p>configure:4386: $? = 0<br>
configure:4375: cc -v >&5<br>
Using built-in specs.<br>
Target: x86_64-redhat-linux<br>
Configured with: ../configure --prefix=/usr
--mandir=/usr/share/man --infodir=/usr/share/info
--with-bugurl=<a class="moz-txt-link-freetext" href="http://bugzilla.redhat.com/bugzilla">http://bugzilla.redhat.com/bugzilla</a>
--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<br>
Thread model: posix<br>
gcc version 4.4.5 20110214 (Red Hat 4.4.5-6) (GCC) <br>
configure:4386: $? = 0<br>
configure:4375: cc -V >&5<br>
cc: '-V' option must have ar gument<br>
configure:4386: $? = 1<br>
configure:4375: cc -qversion >&5<br>
cc: unrecognized option '-qversion'<br>
cc: no input files<br>
configure:4386: $? = 1<br>
configure:4408: checking for C compiler default output file
name<br>
configure:4430: cc conftest.c >&5<br>
configure:4434: $? = 0<br>
configure:4471: result: a.out<br>
configure:4487: checking whether the C compiler works<br>
configure:4496: ./a.out<br>
configure:4500: $? = 0<br>
configure:4515: result: yes<br>
configure:4522: checking whether we are cross compiling<br>
configure:4524: result: no<br>
configure:4527: checking for suffix of executables<br>
configure:4534: cc -o conftest conftest.c >&5<br>
configure:4538: $? = 0<br>
configure:4560: result: <br>
configure:4566: checking for suffix of object files<br>
configure:4588: cc -c conftest.c >&5<br>
configure:4592: $? = 0<br>
configure:4613: result: o<br>
configure:4617: checking whether we are u sing the GNU C
compiler<br>
configure:4636: cc -c conftest.c >&5<br>
configure:4636: $? = 0<br>
configure:4645: result: yes<br>
configure:4654: checking whether cc accepts -g<br>
configure:4674: cc -c -g conftest.c >&5<br>
configure:4674: $? = 0<br>
configure:4715: result: yes<br>
configure:4732: checking for cc option to accept ISO C89<br>
configure:4796: cc -c -g -O2 conftest.c >&5<br>
configure:4796: $? = 0<br>
configure:4809: result: none needed<br>
configure:4840: checking for style of include used by make<br>
configure:4868: result: GNU<br>
configure:4893: checking dependency style of cc<br>
configure:5003: result: gcc3<br>
configure:5262: checking dependency style of cc<br>
configure:5370: result: gcc3<br>
configure:5396: checking for mpxlc<br>
configure:5426: result: no<br>
configure:5396: checking for mpicc<br>
configure:5412: found /usr/lib64/openmpi/bin/mpicc<br>
configure:5423: result: mpicc<br>
configure:5438: checking whether the MPI cc command works<br>
configure:5452: mpicc -o conftest -g -O2 conftest.c
>&5<br>
configure:5452: $? = 0<br>
configure:5453: result: yes<br>
configure:5470: checking for MPI_IN_PLACE in collective
operations<br>
configure:5490: mpicc -c -g -O2 conftest.c >&5<br>
configure:5490: $? = 0<br>
configure:5492: result: yes<br>
configure:5511: checking for catamount<br>
configure:5529: mpicc -c -g -O2 conftest.c >&5<br>
conftest.c:23:2: error: #error not catamount<br>
configure:5529: $? = 1</p>
<p>configure: failed program was:<br>
| /* confdefs.h */<br>
| #define PACKAGE_NAME "gromacs"<br>
| #define PACKAGE_TARNAME "gromacs"<br>
| #define PACKAGE_VERSION "4.5.5"<br>
| #define PACKAGE_STRING "gromacs 4.5.5"<br>
| #define PACKAGE_BUGREPORT "<a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>"<br>
| #define PACKAGE_URL ""<br>
| #define PACKAGE "gromacs"<br>
| #define VERSION "4.5.5"<br>
| #define GMX_SOFTWARE_INVSQRT /**/<br>
| #define GMX_QMMM_GAUSSIAN /**/<br>
| #define GMX_QMMM_ORCA /**/<br>
| #define BUILD_TIME "Thu Sep 22 23:33:40 CST 2011"<br>
| #define BUILD_USER "<a moz-do-not-send="true"
href="mailto:njn@njn-SL">njn@njn-SL</a>"<br>
| #define BUILD_MACHINE "Linux 2.6.32-131.0.15.el6.x86_64
x86_64"<br>
| #define GMX_MPI /**/<br>
| #define GMX_LIB_MPI /**/<br>
| #define MPI_IN_PLACE_EXISTS /**/<br>
| /* end confdefs.h. */<br>
| <br>
| #if defined __QK_USER__<br>
| #else<br>
| #error not catamount<br>
| #endif<br>
| <br>
| int<br>
| main ()<br>
| {<br>
| <br>
| ;<br>
| retu rn 0;<br>
| }<br>
configure:5551: result: no<br>
configure:6229: checking how to run the C preprocessor<br>
configure:6260: mpicc -E conftest.c<br>
configure:6260: $? = 0<br>
configure:6274: mpicc -E conftest.c<br>
conftest.c:22:28: error: ac_nonexistent.h: No such file or
directory<br>
configure:6274: $? = 1<br>
configure: failed program was:<br>
| /* confdefs.h */<br>
.......<br>
--------------------------------------------------------------------------------------------------------------------------------------------<br>
my system is scientific linux, kernel linux
2.6.32-131.0.15.el16.x86_64<br>
my gcc is 4.4.5<br>
my cpu is intel-i7-940 4 cores</p>
<p>?????????????????????????????????????????????????</p>
<p> </p>
<p>> More useful would be the information that you've been
following the <br>
> online installation guide, and what your configure line
was. As it is, <br>
> it looks like you have some problem with the compiler.
Can you compile <br>
> other code?<br>
><br>
> Mark</p>
<p><br>
--<br>
Sincerely yours <br>
Dr Ji-Nan Niu <br>
School of Materials Science and Engineering.<br>
China University of Mining and Technology.<br>
Jiangsu Province, XuZhou 221116<br>
P. R. China</p>
<p> </p>
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