Re: [gmx-users] install problem on IBM powerpc AIX 5.3
Mark Abraham wrote: liu xin wrote: Hi Mark After some search on the web, I found that in AIX OS mpcc is the MPI c compiler, while mpCC is the MPI C++ compiler and mpxlf is the MPI fortran compiler. but when I tried to configure it like: " configure --enable-mpi MPICC=/usr/bin/mpcc", I still got error complaining "Cannot compile and link MPI code with mpcc". Well, look at the last few hundred lines of config.log and see what you find by the way of error messages when configure tries to use mpcc to compile and link. You should also use ./configure to make sure that you are running the configure in the gromacs install directory, not some other configure in your path. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem on IBM powerpc AIX 5.3
liu xin wrote: Hi Mark After some search on the web, I found that in AIX OS mpcc is the MPI c compiler, while mpCC is the MPI C++ compiler and mpxlf is the MPI fortran compiler. but when I tried to configure it like: " configure --enable-mpi MPICC=/usr/bin/mpcc", I still got error complaining "Cannot compile and link MPI code with mpcc". Well, look at the last few hundred lines of config.log and see what you find by the way of error messages when configure tries to use mpcc to compile and link. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem on IBM powerpc AIX 5.3
Hi Mark After some search on the web, I found that in AIX OS mpcc is the MPI c compiler, while mpCC is the MPI C++ compiler and mpxlf is the MPI fortran compiler. but when I tried to configure it like: " configure --enable-mpi MPICC=/usr/bin/mpcc", I still got error complaining "Cannot compile and link MPI code with mpcc". On 10/18/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > > > Hi, thanks for the time > > I asked my administrator, he told me that there was no mpicc installed > on > > p575, the fore mentioned mpcc was the MPI c compiler, but he is not very > > familiar with the AIX OS either, and I will try to explain my problem > more > > clearly: > > > > a. configure --enable-mpi --prefix=/hpc/gmxmpi > > I got a error message: "checking whether the MPI cc command works... > > configure: error: Cannot compile and link MPI code with mpc" > > > > b. export MPICC=/usr/bin/mpcc > > configure --enable-mpi --prefix=/hpc/gmxmpi > > I got the same error message as (1) > > You need an MPI C compiler. Find out its name. I'd expect b) to work if > you use the right name. Otherwise try ./configure --enable-mpi > MPICC=name_of_mpi_c_compiler > > > c. configure --enable-mpi=/usr/bin/mpcc --prefix=/hpc/gmxmpc > > "--enable-mpi=/usr/bin/mpcc" isn't recognized. Read ./configure --help > > Mark > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem on IBM powerpc AIX 5.3
> Hi, thanks for the time > I asked my administrator, he told me that there was no mpicc installed on > p575, the fore mentioned mpcc was the MPI c compiler, but he is not very > familiar with the AIX OS either, and I will try to explain my problem more > clearly: > > a. configure --enable-mpi --prefix=/hpc/gmxmpi > I got a error message: "checking whether the MPI cc command works... > configure: error: Cannot compile and link MPI code with mpc" > > b. export MPICC=/usr/bin/mpcc > configure --enable-mpi --prefix=/hpc/gmxmpi > I got the same error message as (1) You need an MPI C compiler. Find out its name. I'd expect b) to work if you use the right name. Otherwise try ./configure --enable-mpi MPICC=name_of_mpi_c_compiler > c. configure --enable-mpi=/usr/bin/mpcc --prefix=/hpc/gmxmpc "--enable-mpi=/usr/bin/mpcc" isn't recognized. Read ./configure --help Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem on IBM powerpc AIX 5.3
Hi, thanks for the time I asked my administrator, he told me that there was no mpicc installed on p575, the fore mentioned mpcc was the MPI c compiler, but he is not very familiar with the AIX OS either, and I will try to explain my problem more clearly: a. configure --enable-mpi --prefix=/hpc/gmxmpi I got a error message: "checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpc" b. export MPICC=/usr/bin/mpcc configure --enable-mpi --prefix=/hpc/gmxmpi I got the same error message as (1) c. configure --enable-mpi=/usr/bin/mpcc --prefix=/hpc/gmxmpc the configuration ended without error message, but at the end of the configure output, there was no message telling me that I was compiling with MPI support which usaslly does when I compile it on our Linux Cluster. make mdrun I get the error message: "gcc: unrecognized option '-bmaxdata:0x8000" make install-mdrun grompp -f -c -p -o 6np.tpr -sort -shuffle mdrun -v -s 6np.tpr -np 6 -proces 6 -shared_memory then I got the no MPI support error "GROMACS compiled without MPI support - can't do parallel runs" (4) I checked the Makefile and compared it with the one I successfully compiled on our Linux Cluster, found there was no MPI compiler invoked, for example, the 89th line "AS = gcc", 95th line "CC = gcc", 96th line "CCAS = gcc" etc. in fact, this is the first time we try the AIX OS out, we dont even know which is the MPI compiler, maybe the mpcc is not the MPI compiler... I know many of you guys experienced with installation on AIX, any suggestions ? I am totally a newbie... On 10/18/07, Erik Lindahl <[EMAIL PROTECTED]> wrote: > > MPICC is the environment variable (upper case important). It should be set > to the name of your mpi-enabled C compiler. > Cheers, > > ERik > > On Oct 18, 2007, at 4:40 AM, liu xin wrote: > > Hi Erick > you mean export MPICC=mpcc? ok, I will try that > > > > On 10/18/07, Erik Lindahl <[EMAIL PROTECTED]> wrote: > > > > Hi, > > > > On Oct 17, 2007, at 7:13 PM, liu xin wrote: > > > > > Thanks for your quick comment David > > > but if I tried > > > ./configure --enable-mpi --prefix=/hpc/gromacsmpi > > > it will complain about cant find MPI compiler, but I've already > > > export mpcc=mpicc > > > > > > > Try setting MPICC instead :-) > > > > Cheers, > > > > Erik > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem on IBM powerpc AIX 5.3
MPICC is the environment variable (upper case important). It should be set to the name of your mpi-enabled C compiler. Cheers, ERik On Oct 18, 2007, at 4:40 AM, liu xin wrote: Hi Erick you mean export MPICC=mpcc? ok, I will try that On 10/18/07, Erik Lindahl <[EMAIL PROTECTED]> wrote: Hi, On Oct 17, 2007, at 7:13 PM, liu xin wrote: > Thanks for your quick comment David > but if I tried > ./configure --enable-mpi --prefix=/hpc/gromacsmpi > it will complain about cant find MPI compiler, but I've already > export mpcc=mpicc > Try setting MPICC instead :-) Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem on IBM powerpc AIX 5.3
liu xin wrote: Hi Erick you mean export MPICC=mpcc? ok, I will try that No. The name of the mpicc (pseudo) compiler is mpicc. That is also the name of the variable that contains that name - i.e. MPICC Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem on IBM powerpc AIX 5.3
Hi Erick you mean export MPICC=mpcc? ok, I will try that On 10/18/07, Erik Lindahl <[EMAIL PROTECTED]> wrote: > > Hi, > > On Oct 17, 2007, at 7:13 PM, liu xin wrote: > > > Thanks for your quick comment David > > but if I tried > > ./configure --enable-mpi --prefix=/hpc/gromacsmpi > > it will complain about cant find MPI compiler, but I've already > > export mpcc=mpicc > > > > Try setting MPICC instead :-) > > Cheers, > > Erik > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem on IBM powerpc AIX 5.3
Hi, On Oct 17, 2007, at 7:13 PM, liu xin wrote: Thanks for your quick comment David but if I tried ./configure --enable-mpi --prefix=/hpc/gromacsmpi it will complain about cant find MPI compiler, but I've already export mpcc=mpicc Try setting MPICC instead :-) Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem on IBM powerpc AIX 5.3
Thanks for your quick comment David but if I tried ./configure --enable-mpi --prefix=/hpc/gromacsmpi it will complain about cant find MPI compiler, but I've already export mpcc=mpicc On 10/18/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > > liu xin wrote: > > Hello everyone > > > > I tried to install gromacs-3.3.1 on our IBM PowerPC with AIX 5.3 OS, > > this is how I've done it: > > ./configure --enable-mpi=/usr/bin --prefix=/hpc/gromacsmpi > Is this the command line you used? Try: > ./configure --enable-mpi --prefix=/hpc/gromacsmpi > > > make mdrun > > make install-mdrun > > > > then I tried to mdrun my system with 6 cpu > > grompp -f md.mdp -c -p -o 6np.tpr -np 6 -shuffle -sort > > mdrun -v -s 6np.tpr -np 6 -proces 6 -shared_memory > > > > then I get the error message telling me that "the GROMACS was compiled > > with no MPI support", but I can run mdrun with 1 cpu! > > we have installed "Parallel Environment V4.2" and "Parallel Engineering > > and Scienticfic Subroutine Library V3.2" on this machine. I am not > > familiar with the AIX OS, the MPI compiler on our machine is mpcc (I > > dont know for sure) installed in /usr/bin. > > Any suggestions will be REALLY appreciated ! > > > > Yours > > Xin Liu > > > > > > > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem on IBM powerpc AIX 5.3
liu xin wrote: Hello everyone I tried to install gromacs-3.3.1 on our IBM PowerPC with AIX 5.3 OS, this is how I've done it: ./configure --enable-mpi=/usr/bin --prefix=/hpc/gromacsmpi Is this the command line you used? Try: ./configure --enable-mpi --prefix=/hpc/gromacsmpi make mdrun make install-mdrun then I tried to mdrun my system with 6 cpu grompp -f md.mdp -c -p -o 6np.tpr -np 6 -shuffle -sort mdrun -v -s 6np.tpr -np 6 -proces 6 -shared_memory then I get the error message telling me that "the GROMACS was compiled with no MPI support", but I can run mdrun with 1 cpu! we have installed "Parallel Environment V4.2" and "Parallel Engineering and Scienticfic Subroutine Library V3.2" on this machine. I am not familiar with the AIX OS, the MPI compiler on our machine is mpcc (I dont know for sure) installed in /usr/bin. Any suggestions will be REALLY appreciated ! Yours Xin Liu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
