Dear Nuno<br><br>thanks for your helpful suggestion. It worked successful. <br><br>But the following command mpirun -np 2 mdrun_mpi_d -v -s em_1.tpr -c em_1.pdb doesnt seem to run parallely. I have mentiond the output below. <br>
<br>....................<br>bansal@corsica:~/CKC/L2PJR> mpirun -np 2 mdrun_mpi_d -v -s em_1.tpr -c em_1.pdb<br>[corsica:17339] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182<br>--------------------------------------------------------------------------<br>
It looks like orte_init failed for some reason; your parallel process is<br>likely to abort. There are many reasons that a parallel process can<br>fail during orte_init; some of which are due to configuration or<br>environment problems. This failure appears to be an internal failure;<br>
here's some additional information (which may only be relevant to an<br>Open MPI developer):<br><br> orte_rml_base_select failed<br> --> Returned value -13 instead of ORTE_SUCCESS<br><br>--------------------------------------------------------------------------<br>
[corsica:17339] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_system_init.c at line 42<br>[corsica:17339] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 52<br>--------------------------------------------------------------------------<br>
Open RTE was unable to initialize properly. The error occured while<br>attempting to orte_init(). Returned value -13 instead of ORTE_SUCCESS.<br>--------------------------------------------------------------------------<br>
<br clear="all">Chandan<br><br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>
<br><br><div class="gmail_quote">On Fri, Jan 15, 2010 at 5:04 PM, Nuno Azoia <span dir="ltr"><<a href="mailto:nazoia@det.uminho.pt">nazoia@det.uminho.pt</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello!<br>
<br>
I had the same problem, and for me the solution was to set up the<br>
openmpi/lib directory. The compiler is not able to find it alone.<br>
<br>
I'm using bash, so for me the solution was:<br>
<br>
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/your/directory/openmpi/lib<br>
<br>
of course you have to change "/your/directory" with the correct path in<br>
your system.<br>
<br>
I hope this will help.<br>
<br>
Nuno Azoia<br>
<div><div></div><div class="h5"><br>
On Fri, 2010-01-15 at 12:30 +0530, Chandan Choudhury wrote:<br>
> Hello gmx-users !!<br>
><br>
> I am trying to install gromacs 4.0.7 double precision with mpi. I<br>
> downloaded openmpi-1.4. and installed it.<br>
> Then executed<br>
> ./configure --enable-mpi --program-suffix=_mpi_d<br>
> --prefix=/usr/local/gromacs407_double_mpi --enable-double<br>
><br>
> It showed checking for mpicc...<br>
> mpicc<br>
> checking whether the MPI cc command works...<br>
> yes<br>
> checking for catamount...<br>
> no<br>
> checking how to run the C preprocessor... mpicc<br>
> -E<br>
> checking whether mpicc accepts -O3...<br>
> yes<br>
> checking whether mpicc accepts -funroll-all-loops...<br>
> yes<br>
> checking whether mpicc accepts -O3 -fomit-frame-pointer<br>
> -finline-functions -Wall -Wno-unused -funroll-all-loops...<br>
> yes<br>
> checking for grep that handles long lines and<br>
> -e... /usr/bin/grep<br>
> checking for egrep... /usr/bin/grep<br>
> -E<br>
> checking for ANSI C header files...<br>
> no<br>
> checking for sys/types.h...<br>
> yes<br>
> checking for sys/stat.h...<br>
> yes<br>
> checking for stdlib.h...<br>
> yes<br>
> checking for string.h...<br>
> yes<br>
> checking for memory.h...<br>
> yes<br>
> checking for strings.h...<br>
> yes<br>
> checking for inttypes.h...<br>
> yes<br>
> checking for stdint.h...<br>
> yes<br>
> checking for unistd.h...<br>
> yes<br>
> checking whether byte ordering is bigendian...<br>
> no<br>
> checking for int...<br>
> yes<br>
> checking size of int... configure: error: cannot compute sizeof<br>
> (int)<br>
> See `config.log' for more details.<br>
><br>
> The part of the config.log reads as:<br>
><br>
> --configure:4577: checking whether the MPI cc command works<br>
> configure:4601: mpicc -o conftest -g -O2 conftest.c >&5<br>
> configure:4607: $? = 0<br>
> configure:4613: result: yes<br>
> configure:4636: checking for catamount<br>
> configure:4664: mpicc -c -g -O2 conftest.c >&5<br>
> conftest.c:20:2: error: #error not catamount<br>
> configure:4670: $? = 1<br>
> configure: failed program was:<br>
> | /* confdefs.h. */<br>
> | #define PACKAGE_NAME "gromacs"<br>
> | #define PACKAGE_TARNAME "gromacs"<br>
> | #define PACKAGE_VERSION "4.0.7"<br>
> | #define PACKAGE_STRING "gromacs 4.0.7"<br>
> | #define PACKAGE_BUGREPORT "<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>"<br>
> | #define PACKAGE "gromacs"<br>
> | #define VERSION "4.0.7"<br>
> | #define GMX_DOUBLE<br>
> | #define GMX_SOFTWARE_SQRT<br>
> | #define GMX_QMMM_GAUSSIAN<br>
> | #define BUILD_TIME "Sun Jan 17 01:26:27 EST 2010"<br>
> | #define BUILD_USER "root@corsica"<br>
> | #define BUILD_MACHINE "Linux 2.6.31.5-0.1-desktop i686"<br>
> | #define GMX_MPI<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>
> | return 0;<br>
> | }<br>
> configure:4706: result: no<br>
> configure:5590: checking how to run the C preprocessor<br>
> configure:5630: mpicc -E conftest.c<br>
> configure:5636: $? = 0<br>
> configure:5667: mpicc -E conftest.c<br>
> conftest.c:19:28: error: ac_nonexistent.h: No such file or directory<br>
> |<br>
> | int<br>
> | main ()<br>
> | {<br>
> |<br>
> | ;<br>
> | return 0;<br>
> | }<br>
> configure:4706: result: no<br>
> configure:5590: checking how to run the C preprocessor<br>
> configure:5630: mpicc -E conftest.c<br>
> configure:5636: $? = 0<br>
> configure:5667: mpicc -E conftest.c<br>
> conftest.c:19:28: error: ac_nonexistent.h: No such file or directory<br>
> configure:5673: $? = 1<br>
> configure: failed program was:<br>
> | /* confdefs.h. */<br>
> | #define PACKAGE_NAME "gromacs"<br>
> | #define PACKAGE_TARNAME "gromacs"<br>
> | #define PACKAGE_VERSION "4.0.7"<br>
> | #define PACKAGE_STRING "gromacs 4.0.7"<br>
> | #define PACKAGE_BUGREPORT "<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>"<br>
> | #define PACKAGE "gromacs"<br>
> | #define VERSION "4.0.7"<br>
> | #define GMX_DOUBLE<br>
> | #define GMX_SOFTWARE_SQRT<br>
> | #define GMX_QMMM_GAUSSIAN<br>
> | #define BUILD_TIME "Sun Jan 17 01:26:27 EST 2010"<br>
> | #define BUILD_USER "root@corsica"<br>
> | #define BUILD_MACHINE "Linux 2.6.31.5-0.1-desktop i686"<br>
> | #define GMX_MPI<br>
> | #define F77_OR_C_FUNC(name,NAME) name<br>
> | #define F77_OR_C_FUNC_(name,NAME) name<br>
> | /* end confdefs.h. */<br>
> | #include <ac_nonexistent.h><br>
> configure:5706: result: mpicc -E<br>
> configure:5735: mpicc -E conftest.c<br>
> configure:5741: $? = 0<br>
> configure:5772: mpicc -E conftest.c<br>
> conftest.c:19:28: error: ac_nonexistent.h: No such file or directory<br>
> ..............................................................................................<br>
> ..............................................................................................<br>
> configure:6203: checking whether mpicc accepts -O3<br>
> configure:6221: result: yes<br>
> configure:6501: checking whether mpicc accepts -funroll-all-loops<br>
> configure:6519: result: yes<br>
> configure:6558: checking whether mpicc accepts -O3<br>
> -fomit-frame-pointer -finline-functions -Wall -Wno-unused<br>
> -funroll-all-loops<br>
> configure:6576: result: yes<br>
> configure:6668: checking for grep that handles long lines and -e<br>
> configure:6742: result: /usr/bin/grep<br>
> configure:6747: checking for egrep<br>
> configure:6825: result: /usr/bin/grep -E<br>
> configure:6830: checking for ANSI C header files<br>
> configure:6868: mpicc -c -O3 -fomit-frame-pointer -finline-functions<br>
> -Wall -Wno-unused -funroll-all-loops conftest.c >&5<br>
> configure:6874: $? = 0<br>
> configure:6973: mpicc -o conftest -O3 -fomit-frame-pointer<br>
> -finline-functions -Wall -Wno-unused -funroll-all-loops conftest.c<br>
> >&5<br>
> configure:6976: $? = 0<br>
> configure:6982: ./conftest<br>
> ./conftest: error while loading shared libraries: libmpi.so.0: cannot<br>
> open shared object file: No such file or directory<br>
> configure:6985: $? = 127<br>
> configure: program exited with status 127<br>
><br>
> I also searched the gmx-users list, but cant understand it. Google<br>
> also didnt help me.<br>
><br>
> Looking forward from you all.<br>
><br>
> Chandan<br>
><br>
> --<br>
> Chandan kumar Choudhury<br>
> NCL, Pune<br>
> INDIA<br>
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