[gmx-users] install problem of ngmx
Hello,nbsp; my configurenbsp;line is ./configure --without-Xnbsp; --enable-mpi --enable-fortran --prefix=/mnt/soft/chemtec/gromacs4.0.5. I have been settednbsp; in the ~/.bashrc like this : nbsp; export PATH=/opt/mpich2wgs/bin:$PATH:/share/apps/intel/fce/10.1.022/bin export CC=gcc export CXX=g++ export CFLAGS=-03 xport CXXFLAGS=-03 export FFLAGS=-03 export CPPFLAGS=-I/mnt/soft/chemtec/fftw3.2.1/include export LDFLAGS=-L/ mnt/soft/chemtec/fftw3.2.1/lib exportnbsp;nbsp;nbsp;nbsp;nbsp;F77=ifort export LD_LIBRARY_PATH=/opt/mpich2wgs/lib/:$LD_LIBRARY_PATH the version of the gcc is 4.1.1. Thank you!-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem of ngmx
kecy...@sina.com wrote: Hello, my configure line is ./configure --without-X --enable-mpi --enable-fortran --prefix=/mnt/soft/chemtec/gromacs4.0.5. I have been setted in the ~/.bashrc like this : --without-X and --without-x are different things. Computers are literal. Watch the output of ./configure to see if it complains about not finding X headers and libraries instead of simply saying disabled (which you should get if you ./configure --without-x). -Justin /export PATH=/opt/mpich2wgs/bin:$PATH:/share/apps/intel/fce/10.1.022/bin/ /export CC=gcc export CXX=g++ export CFLAGS=-03 xport CXXFLAGS=-03 export FFLAGS=-03 / /export CPPFLAGS=-I/mnt/soft/chemtec/fftw3.2.1/include export LDFLAGS=-L/ mnt/soft/chemtec/fftw3.2.1/lib/ /export F77=ifort/ /export LD_LIBRARY_PATH=/opt/mpich2wgs/lib/:$LD_LIBRARY_PATH/ the version of the gcc is 4.1.1. Thank you! -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem of ngmx
kecy...@sina.com wrote: the version of the gcc is 4.1.1. Get a better version of gcc. Note the prominent warning on the Downloads page: http://www.gromacs.org/index.php?title=Download_%26_Installation -Justin Thank you! -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] install problem of ngmx
Hello, the error is like that : *Innbsp;filenbsp;includednbsp;fromnbsp;ngmx.c:50:* nbsp;*Xstuff.h:48:22:nbsp;error:nbsp;X11/Xlib.h:nbsp;Nonbsp;suchnbsp;filenbsp;ornbsp;directory* nbsp;*Xstuff.h:49:23:nbsp;error:nbsp;X11/Xutil.h:nbsp;Nonbsp;suchnbsp;filenbsp;ornbsp;directory* nbsp;*Xstuff.h:51:28:nbsp;error:nbsp;X11/cursorfont.h:nbsp;Nonbsp;suchnbsp;filenbsp;ornbsp;directory* nbsp;*Xstuff.h:52:27:nbsp;error:nbsp;X11/Xresource.h:nbsp;Nonbsp;suchnbsp;filenbsp;ornbsp;directory* nbsp;but in my system, it has the Xlib.h,Xutil.h,cursorfont.h,Xresource.h in the /usr/X11R6/include /X11 file. Wherenbsp; I should put these documents in can it finds?-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem of ngmx
On 13/04/2010 12:14 AM, kecy...@sina.com wrote: Hello, the error is like that : *In file included from ngmx.c:50:* *Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory* *Xstuff.h:49:23: error: X11/Xutil.h: No such file or directory* *Xstuff.h:51:28: error: X11/cursorfont.h: No such file or directory* *Xstuff.h:52:27: error: X11/Xresource.h: No such file or directory* but in my system, it has the Xlib.h,Xutil.h,cursorfont.h,Xresource.h in the /usr/X11R6/include /X11 file. Where I should put these documents in can it finds? Don't move the files anywhere. That way madness lies. Justin told you how to use --without-x properly. Do that, or use CFLAGS=-I/usr/X11R6/include/X11 properly. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem of ngmx.
On 8/04/2010 5:52 PM, kecy...@sina.com wrote: Hello, I installed the gromacs4.0.5, when I made, it had lots of mistakes, below is some of the mistakes: You should prefer to install the latest version, not one that's over a year old. Bugs get fixed... Unless you're planning to use ngmx you can use ./configure --without-X and this problem will go away. configure should really have recognized that ngmx couldn't be compiled. If you've not run configure on this machine in the same shell from which you try to make, go and do that properly. If you have done this properly, then you have something unique about your machine... Mark /In file included from ngmx.c:50:/ /Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory/ /Xstuff.h:49:23: error: X11/Xutil.h: No such file or directory/ /Xstuff.h:51:28: error: X11/cursorfont.h: No such file or directory/ /Xstuff.h:52:27: error: X11/Xresource.h: No such file or directory/ /In file included from ./xutil.h:43,/ /from ./xdlgitem.h:42,/ /from xdlg.h:40,/ /from dialogs.h:40,/ /from ngmx.c:54:/ /./x11.h:57: error: expected specifier-qualifier-list before 'Display'/ /./x11.h:79: error: expected declaration specifiers or '...' before 'XEvent'/ /./x11.h:79: error: expected declaration specifiers or '...' before 'Window'/ /./x11.h:82: error: expected specifier-qualifier-list before 'Window'/ /In file included from ./xdlgitem.h:42,/ /from xdlg.h:40,/ /from dialogs.h:40,/ /from ngmx.c:54:/ /./xutil.h:49: error: expected specifier-qualifier-list before 'Window'/ /./xutil.h:57: error: expected ')' before 'win'/ /./xutil.h:61: error: expected ')' before '*' token/ /./xutil.h:63: error: expected declaration specifiers or '...' before 'XFontStruct'/ /./xutil.h:63: error: expected declaration specifiers or '...' before 'Drawable'/ /./xutil.h:67: error: expected declaration specifiers or '...' before 'Drawable'/ /./xutil.h:75: error: expected ')' before '*' token/ /./xutil.h:77: error: expected ')' before '*' token/ /./xutil.h:79: error: expected ')' before '*' token/ /./xutil.h:81: error: expected ')' before '*' token/ /./xutil.h:84: error: expected ')' before '*' token/ /./xutil.h:87: error: expected ')' before '*' token/ /./xutil.h:89: error: expected ')' before '*' token/ /./xutil.h:91: error: expected ')' before '*' token/ /In file included from xdlg.h:40,/ /from dialogs.h:40,/ /from ngmx.c:54:/ /./xdlgitem.h:66: error: expected specifier-qualifier-list before 'Pixmap'/ /./xdlgitem.h:98: error: expected declaration specifiers or '...' before 'XEvent'/ /./xdlgitem.h:142: error: expected declaration specifiers or '...' before 'Pixmap'/ /In file included from dialogs.h:40,/ /from ngmx.c:54:/ /xdlg.h:63: error: expected specifier-qualifier-list before 'Window'/ /xdlg.h:81: error: expected declaration specifiers or '...' before 'Window'/ /xdlg.h:140: error: expected declaration specifiers or '...' before 'Window'/ /In file included from pulldown.h:40,/ /from dialogs.h:41,/ /from ngmx.c:54:/ /popup.h:44: error: expected specifier-qualifier-list before 'Window'/ /popup.h:53: error: expected specifier-qualifier-list before 'Window'/ /popup.h:58: error: expected specifier-qualifier-list before 'Window'/ /popup.h:64: error: expected declaration specifiers or '...' before 'Window'/ /In file included from dialogs.h:41,/ /from ngmx.c:54:/ /pulldown.h:51: error: expected declaration specifiers or '...' before 'Window'/ /In file included from manager.h:45,/ /from dialogs.h:42,/ /from ngmx.c:54:/ /nleg.h:54: error: expected declaration specifiers or '...' before 'Window'/ /In file included from manager.h:46,/ /from dialogs.h:42,/ /from ngmx.c:54:/ /buttons.h:64: error: expected declaration specifiers or '...' before 'Window'/ /buttons.h:64: error: expected declaration specifiers or '...' before 'Window'/ /buttons.h:69: error: expected declaration specifiers or '...' before 'Window'/ /buttons.h:69: error: expected declaration specifiers or '...' before 'Window'/ /In file included from dialogs.h:42,/ /from ngmx.c:54:/ /manager.h:133: error: expected declaration specifiers or '...' before 'Window'/ /In file included from dialogs.h:43,/ /from ngmx.c:54:/ /logo.h:44: error: expected specifier-qualifier-list before 'XFontStruct'/ /logo.h:53: error: expected declaration specifiers or '...' before 'Window'/ /In file included from ngmx.c:57:/ /nmol.h:43: error: expected declaration specifiers or '...' before 'Window'/ /ngmx.c:65: error: expected declaration specifiers or '...' before 'Window'/ /ngmx.c: In function 'dump_xw':/ /ngmx.c:70: error: 'w' undeclared (first use in this function)/ /ngmx.c:70: error: (Each undeclared identifier is reported only once/ /ngmx.c:70: error: for each function it appears in.)/ /ngmx.c:411: error: 't_x11' has no member named 'bg'/ /ngmx.c:412: warning: passing argument 7 of 'init_pd' makes pointer from integer without a cast/ /ngmx.c:412: warning: passing argument 8 of
Re: [gmx-users] install problem
Hi, search in config.log for the compiler error. This should tell you the problem. If not post the compiler error. Roland On Tue, Apr 7, 2009 at 5:20 AM, Hongyan Xiao hyx...@mail.ipc.ac.cn wrote: Dear gmx-users, When I parallel install gromacs-4.0.4 using my own usr. I encountered the problem. The following is my installation steps. Step 1: install lam-7.1.4 $ cd lam-7.1.4 $ ./configure --prefix=/home/xhy/software/lam-7.1.4 --without-fc --with-rsh=ssh-x $ make $ make install then adding /home/xhy/software/lam-7.1.4/bin into .bashrc file. $ source .bashrc Step 2: install fftw-3.1.2 $ cd fftw-3.1.2 $ ./configure --prefix=/home/xhy/software/fftw-3.1.2 --enable-float --enable-threads $ make $ make install then adding /home/xhy/software/fftw-3.1.2/bin, export CPPFLAGS==-I/home/xhy/software/fftw-3.1.2/include and export LDFLAGS=-L/home/xhy/software/fftw-3.1.2/lib into .bashrc file. $ source .bashrc Step 3: install gromacs-4.0.4 $ cd gromacs-4.0.4 $./configure --prefix=/home/xhy/software/gromacs-4.0.4 --exec-prefix=/home/xhy/software/gromacs-4.0.4 --enable-mpi --with-fftw3 --program-suffix=_mpi then I encountered the following errors: checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p 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... configure: error: C compiler cannot create executables See `config.log' for more details. Can you help me? I hope for your answer. Thank you very much! H.Y. Xiao ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] install problem
Dear gmx-users, When I parallel install gromacs-4.0.4 using my own usr. I encountered the problem. The following is my installation steps. Step 1: install lam-7.1.4 $ cd lam-7.1.4 $ ./configure --prefix=/home/xhy/software/lam-7.1.4 --without-fc --with-rsh=ssh-x $ make $ make install then adding /home/xhy/software/lam-7.1.4/bin into .bashrc file. $ source .bashrc Step 2: install fftw-3.1.2 $ cd fftw-3.1.2 $ ./configure --prefix=/home/xhy/software/fftw-3.1.2 --enable-float --enable-threads $ make $ make install then adding /home/xhy/software/fftw-3.1.2/bin, export CPPFLAGS==-I/home/xhy/software/fftw-3.1.2/include and export LDFLAGS=-L/home/xhy/software/fftw-3.1.2/lib into .bashrc file. $ source .bashrc Step 3: install gromacs-4.0.4 $ cd gromacs-4.0.4 $./configure --prefix=/home/xhy/software/gromacs-4.0.4 --exec-prefix=/home/xhy/software/gromacs-4.0.4 --enable-mpi --with-fftw3 --program-suffix=_mpi then I encountered the following errors: checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p 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... configure: error: C compiler cannot create executables See `config.log' for more details. Can you help me? I hope for your answer. Thank you very much! H.Y. Xiao ___ 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 gmx-users-requ...@gromacs.org. 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
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 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
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
[gmx-users] install problem on IBM powerpc AIX 5.3
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 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
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
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
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
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
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
[gmx-users] install problem
Hi, I am a beginning user of GROMACS, and am just now trying to get a functional installation. There is something not quite right about the installations I have tried. I have spent considerable time testing ideas about what might be the problem, but have not nailed it. I am hoping someone will have a suggestion (perhaps obvious) that will reduce the time I am spending getting GROMACS operational. I can duplicate the problem with multiple GROMACS subprograms but will only refer to luck (luck.c). Platform: Mac OS X 10.4.10 Installations tried: 1. Binary package install of gromacs-3.3.dmg.gz (from www.gromacs.org) 2. Fink with compile; first standalone, then remove standalone and install openmpi In both cases, GMXRC.bash is sourced in profile. 3. All installations exhibit the same problem so I'll stick to fink. Indications: 1. luck -c executes with a segmentation fault from any directory. 2. /sw/bin/luck -c executes normally from any directory. (/usr/local/ bin installation exhibits same problem.) 3. Not a UNIX PATH problem as non GROMACS functions in /sw/bin execute normally from the same shell. 4. A shorter PATH value does function normally without regard to where fink subdirectories are placed in the PATH, causing me to wonder whether PATH is parsed in code with a fixed memory variable. Diagnostics: 1. luck -c prints the GROMACS banner before it's segmentation fault 2. /sw/bin/luck -c prints the banner, a wording for the GROMACS acronym, a version number, the authors, software information, and a user friendly quote. 3. Comparing 1. 2. with luck.c, copyrite.c, etc suggestions that a call to bromacs() in CopyRight() migh be where the problem manifests itself. 4. The call sequence could be CopyRight() - bromacs() - pukeit() - low_lib_libopen() - low_libfn(). 5. Note: I haven't tested all these functions to verify they are each involved, but suggest them as a hypothesis based on the output and looking at traces of system calls. 6. One thing that puzzles me is that it looks as if low_libfn() expects GMXLIB as an environment variable, but the script GMXRC.bash sets up GMXLDLIB as the library environment variable. Whatever the problem, the program executes from any directory, but only with the full path specified does it execute without a segmentation fault. Any advice on how to fix this problem would be greatly appreciated. John Mercer ___ 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
John Mercer wrote: Hi, I am a beginning user of GROMACS, and am just now trying to get a functional installation. There is something not quite right about the installations I have tried. I have spent considerable time testing ideas about what might be the problem, but have not nailed it. I am hoping someone will have a suggestion (perhaps obvious) that will reduce the time I am spending getting GROMACS operational. I can duplicate the problem with multiple GROMACS subprograms but will only refer to luck (luck.c). Platform: Mac OS X 10.4.10 Installations tried: 1. Binary package install of gromacs-3.3.dmg.gz (from www.gromacs.org) 2. Fink with compile; first standalone, then remove standalone and install openmpi In both cases, GMXRC.bash is sourced in profile. 3. All installations exhibit the same problem so I'll stick to fink. Indications: 1. luck -c executes with a segmentation fault from any directory. 2. /sw/bin/luck -c executes normally from any directory. (/usr/local/bin installation exhibits same problem.) 3. Not a UNIX PATH problem as non GROMACS functions in /sw/bin execute normally from the same shell. 4. A shorter PATH value does function normally without regard to where fink subdirectories are placed in the PATH, causing me to wonder whether PATH is parsed in code with a fixed memory variable. Diagnostics: 1. luck -c prints the GROMACS banner before it's segmentation fault 2. /sw/bin/luck -c prints the banner, a wording for the GROMACS acronym, a version number, the authors, software information, and a user friendly quote. 3. Comparing 1. 2. with luck.c, copyrite.c, etc suggestions that a call to bromacs() in CopyRight() migh be where the problem manifests itself. 4. The call sequence could be CopyRight() - bromacs() - pukeit() - low_lib_libopen() - low_libfn(). 5. Note: I haven't tested all these functions to verify they are each involved, but suggest them as a hypothesis based on the output and looking at traces of system calls. 6. One thing that puzzles me is that it looks as if low_libfn() expects GMXLIB as an environment variable, but the script GMXRC.bash sets up GMXLDLIB as the library environment variable. Whatever the problem, the program executes from any directory, but only with the full path specified does it execute without a segmentation fault. Any advice on how to fix this problem would be greatly appreciated. have you tried using csh? csh source .../bin/GMXRC just guessing at this point, but on my mac it works fins under a c-shell, an always has. -- 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] install problem
Dear GMX List, I am running into an installation problem with a recent version of the pathscale compiler when trying ./configure --enable-mpi I get checking size of int... configure: error: cannot compute sizeof (int), 77 I searched the list and saw a similar problem with xlc, but no solution.. Is there a workaround for this? Jim Rustad ___ 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
