[gmx-users] gromacs parallel problem
Dear All, I configured gromacs 3.3.3 for parallel runs, using the precompiled packeges on ubuntu server 8.04, with LAM program 7.1.2 ( alreay present in server verison). I tried with d.villin benchmark but I detected an decrease of performance increasing the node's number. The obtained results for 1 node are: (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 6.686 1.437 8.471 2.833 The obtained results for 7 nodes are: (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 5.169 1.112 6.545 3.667 I have a cluster of 7 nodes (pentium 4 3.2 Ghz with RAM 2Gb) connected on 10/100 Mbps dual speed up hub. I don't know if it is a configuration problem (because with precompiled packages I couldn't use the configuration parameters described on web) or an hardware problem due to hub. Please can you help me? Is possible to improve performance changing some other parameters or configuration settings? Thank you in advance Best regards Mario Unisciti alla community di Io fotografo e video, il nuovo corso di fotografia di Gazzetta dello sport: http://www.flickr.com/groups/iofotografoevideo___ 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] problem with mpi configuration.
Thank you very much for help me. I have try to install gromacs 3.3.3 on rhel 4.0. I try to configure gromacs single with the command "./configure --enable-mpi --program-suffix=_mpi--prefix=/usr/local/gromacs332", but when I try to install, I have this error: usr/bin/install: cannot create regular file `/usr/local/gromacs/bin/grompp_mpi_d--prefix=/usr/local/gromacs333': No such file or directory make[3]: *** [install-binPROGRAMS] Error 1 make[3]: Leaving directory `/home/mario/gromacs-3.3.3/src/kernel' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/mario/gromacs-3.3.3/src/kernel' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/home/mario/gromacs-3.3.3/src' make: *** [install-recursive] Error 1 I have try to edit the end of the configure command "/usr/local/gromacs332" with"/usr/local/gromacs333" and "/usr/local/gromacs" but I have anlogue errors. Can you help me? Thanks in advance. Mario Diego Enry <[EMAIL PROTECTED]> ha scritto: You should check the user guide. http://www.mcs.anl.gov/research/projects/mpich2/documentation/index.php?s=docs In a nutshell: 1) You need is to install mpich in all machines. Actually you can sync the mpich install directory (also gromacs). 2) You also need to have the same /etc/hosts on every machine. rsync that. 3) You need to grant ssh access without password by creating a rsa-key for every user Fell free to private message if you need any additional help. Ciao. On Tue, Mar 4, 2008 at 6:04 AM, mario ciappy wrote: > Thank's Diego, > I'm grateful to you. I have only one question. How can I configure mpi/lam > for relaize the comunication between nodes? > I have created an hostsfile with my ip addresses. > Thank's a lot in advance. > > Mario > > Diego Enry ha scritto: > > Since you didn't show us the problems you met.. try following this: > > #1) Download essential packages > #1.1) mpich > wget > http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/mpich2-1.0.6p1.tar.gz > > #1.2) fftw > wget ftp://ftp.fftw.org/pub/fftw/fftw-3.1.2.tar.gz > > #1.3) gromacs > wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.2.tar.gz > > > #2) compile packages: > > #2.1) mpich > tar xvfz mpich2-1.0.6p1.tar.gz > cd mpich2-1.0.6p1 > make distclean > ./configure --with-device=ch3:nemesis --enable-fast --disable-cxx > --enable-error-checking=no CFLAGS=-O3 FFLAGS=-O3 > make > make install > make distclean > cd .. > > #2.2) fftw single > tar xvfz fftw-3.1.2.tar.gz > cd fftw-3.1.2 > make distclean > ./configure --enable-float --enable-sse --enable-threads > make > make install > make distclean > cd .. > > #2.3) gromacs single > tar xvfz gromacs-3.3.2.tar.gz > cd gromacs-3.3.2 > ./configure --enable-mpi --program-suffix=_mpi > --prefix=/usr/local/gromacs332 > make > make install > make links > make distclean > cd .. > > #2.4) fftw double > cd fftw-3.1.2 > ./configure --enable-sse2 --enable-threads > make > make install > make distclean > cd .. > > #2.2) gromacs double > cd gromacs-3.3.2 > ./configure --enable-mpi --program-suffix=_mpi_d > --prefix=/usr/local/gromacs332 --enable-double > make > make install > make links > make distclean > cd .. > > > > > On Mon, Mar 3, 2008 at 3:09 PM, mario ciappy wrote: > > Dear all, > > I'm tried to configure gromacs in parallel but I have meet some problems. > > I don't understand if the problems are relative to mpi or gromacs > > configuration. For this reason I'd be grateful if you explained a detailed > > installation procedure of all that require to run gromacs in parallel, > > started by mpi/lam configuration. I now that is an hard and demanding > > request, but it is a big help for me because you are only resource. > > > > Thank's in advance > > > > Mario > > > > > > > > > > > > L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail > > ___ > > gmx-users mailing list gmx-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 > > > > > > -- > Diego Enry B. Gomes > Laboratório de Modelagem e Dinamica Molecular > Universidade Federal do
Re: [gmx-users] problem with mpi configuration.
Thank's Diego, I'm grateful to you. I have only one question. How can I configure mpi/lam for relaize the comunication between nodes? I have created an hostsfile with my ip addresses. Thank's a lot in advance. Mario Diego Enry <[EMAIL PROTECTED]> ha scritto: Since you didn't show us the problems you met.. try following this: #1) Download essential packages #1.1) mpich wget http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/mpich2-1.0.6p1.tar.gz #1.2) fftw wget ftp://ftp.fftw.org/pub/fftw/fftw-3.1.2.tar.gz #1.3) gromacs wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.2.tar.gz #2) compile packages: #2.1) mpich tar xvfz mpich2-1.0.6p1.tar.gz cd mpich2-1.0.6p1 make distclean ./configure --with-device=ch3:nemesis --enable-fast --disable-cxx --enable-error-checking=no CFLAGS=-O3 FFLAGS=-O3 make make install make distclean cd .. #2.2) fftw single tar xvfz fftw-3.1.2.tar.gz cd fftw-3.1.2 make distclean ./configure --enable-float --enable-sse --enable-threads make make install make distclean cd .. #2.3) gromacs single tar xvfz gromacs-3.3.2.tar.gz cd gromacs-3.3.2 ./configure --enable-mpi --program-suffix=_mpi --prefix=/usr/local/gromacs332 make make install make links make distclean cd .. #2.4) fftw double cd fftw-3.1.2 ./configure --enable-sse2 --enable-threads make make install make distclean cd .. #2.2) gromacs double cd gromacs-3.3.2 ./configure --enable-mpi --program-suffix=_mpi_d --prefix=/usr/local/gromacs332 --enable-double make make install make links make distclean cd .. On Mon, Mar 3, 2008 at 3:09 PM, mario ciappy wrote: > Dear all, > I'm tried to configure gromacs in parallel but I have meet some problems. > I don't understand if the problems are relative to mpi or gromacs > configuration. For this reason I'd be grateful if you explained a detailed > installation procedure of all that require to run gromacs in parallel, > started by mpi/lam configuration. I now that is an hard and demanding > request, but it is a big help for me because you are only resource. > > Thank's in advance > > Mario > > > > > > L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail > ___ > 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 > -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. ___ 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 - - L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail___ 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] problem with mpi configuration.
Dear all, I'm tried to configure gromacs in parallel but I have meet some problems. I don't understand if the problems are relative to mpi or gromacs configuration. For this reason I'd be grateful if you explained a detailed installation procedure of all that require to run gromacs in parallel, started by mpi/lam configuration. I now that is an hard and demanding request, but it is a big help for me because you are only resource. Thank's in advance Mario - - L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail___ 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] Fatal error: moleculetype DPC is redefined.
Hello everyone, when I try to minimise peptide-DPC system with grompp command, I find the error "Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 891 Fatal error: moleculetype DPC is redefined. I produced the dpc.itp file with dundee server. Can you help me? Thanks in advance. Mario __ Do You Yahoo!? Poco spazio e tanto spam? Yahoo! Mail ti protegge dallo spam e ti da tanto spazio gratuito per i tuoi file e i messaggi http://mail.yahoo.it ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] "DPC" not found in residue topology database
mario ciappy <[EMAIL PROTECTED]> ha scritto: Hello everyone,I would start a dynamical study with DPC micelles and peptides, but the DPC is not mentioned in topology database.I imported the dpc.itp file in /usr/local/gromacs/share/gromacs/top/ , but this is not enough: in fact, when I start converting the pdb file, I find the error "DPC not found in residue topology database". Can you suggest me a procedure to upload Gromacs topology database with a new molecule?Thank's in advance Best regardsmusem Chiacchiera con i tuoi amici in tempo reale! http://it.yahoo.com/mail_it/foot/*http://it.messenger.yahoo.com ___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 Chiacchiera con i tuoi amici in tempo reale! http://it.yahoo.com/mail_it/foot/*http://it.messenger.yahoo.com ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] "DPC" not found in residue topology database
mario ciappy <[EMAIL PROTECTED]> ha scritto: Hello everyone,I would start a dynamical study with DPC micelles and peptides, but the DPC is not mentioned in topology database.I imported the dpc.itp file in /usr/local/gromacs/share/gromacs/top/ , but this is not enough: in fact, when I start converting the pdb file, I find the error "DPC not found in residue topology database". Can you suggest me a procedure to upload Gromacs topology database with a new molecule?Thank's in advance Best regardsmusem Chiacchiera con i tuoi amici in tempo reale! http://it.yahoo.com/mail_it/foot/*http://it.messenger.yahoo.com ___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 Chiacchiera con i tuoi amici in tempo reale! http://it.yahoo.com/mail_it/foot/*http://it.messenger.yahoo.com ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] "DPC" not found in residue topology database
mario ciappy <[EMAIL PROTECTED]> ha scritto: Hello everyone,I would start a dynamical study with DPC micelles and peptides, but the DPC is not mentioned in topology database.I imported the dpc.itp file in /usr/local/gromacs/share/gromacs/top/ , but this is not enough: in fact, when I start converting the pdb file, I find the error "DPC not found in residue topology database". Can you suggest me a procedure to upload Gromacs topology database with a new molecule?Thank's in advance Best regardsmusem Chiacchiera con i tuoi amici in tempo reale! http://it.yahoo.com/mail_it/foot/*http://it.messenger.yahoo.com ___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 Chiacchiera con i tuoi amici in tempo reale! http://it.yahoo.com/mail_it/foot/*http://it.messenger.yahoo.com ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] "XXX" not found in residue topology database
Hello everyone,I would start a dynamical study with DPC micelles and peptides, but the DPC is not mentioned in topology database.I have imported the dpc.itp file in /usr/local/gromacs/share/gromacs/top/ , but this is not enough. Why? What is the procedure in this case? Best regardsmusem Chiacchiera con i tuoi amici in tempo reale! http://it.yahoo.com/mail_it/foot/*http://it.messenger.yahoo.com ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
