Re: [gmx-users] MPI problem------Cannot compile and link MPI code with cc
Hi guys I have been running gromacs for a few months now with no real problems however some of my numbers differ from my supervisor's who uses DL-POLY. Anyway discussion of the discrpnacies has led me to questioning aspects of my topology file below (exerpts). We created the topology ourselves. I always thought that the set up below would calculate 1-4 interactions, but having read through the archives I am now confused. Do I have to give a pair list in topology file, or is gen-pairs = yes sufficient. I never created a pairlist as I thought that gen-pairs would create it from the parameters in atomtypes. ;Parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3yes 0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.390500 0.732200 C2 14.027000 0.00 A 0.390500 0.493712 ;Molecular level [moleculetype] ; name nrexcl subhexylcage 3 [atoms] ; atomnr type resnr residue namecgnr charge mass 1 CA 1CGE CA 1 -0.1150 12.0110 2 CB 1CGE CB 1 0. 12.0110 [bonds] ; aiaj func b0(nm) kb(kjmol-1 nm-2) 1 2 1 0.1400 392459.2 1 6 1 0.1400 392459.2 [angles] ; aiajak func theta(deg)ktheta(kjmol-1 rad-2) 2 1 6 1 120.00 711.2800 2 1 7 1 120.00 292.8800 [dihedrals] ; aiajakalfunc V1 V2 V3V4 (all kj mol-1) 1 2 3 4 5 0.0 30.33400 0.0 0.0 1 2 310 5 0.0 30.33400 0.0 0.0 ;System level [system] ;the name of this system config test of 32 subhexyl cage molecules [molecules] ; moleculename number subhexylcage32 -- 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] MPI problem——Cannot compi le and link MPI code with cc
On 29/03/2010 10:24 PM, DreamCatcher wrote: Hello gmx-users, I am trying to install a MPI version of Gromacs that I come across some problems as follows: [cele...@celeste gromacs-4.0.7]$ sudo ./configure --prefix=/home/programmes/gromacs --disable-float --enable-mpi Don't use sudo for configure. It doesn't need it and you risk trashing your system if something in configure doesn't work quite right. Use sudo for the "make install" step only. This is not the cause of your problem, however. checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-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... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... no checking for mpcc... no checking for hcc... no checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with cc I have installed MPICH2 in my PC and export the PATH where the mpicc is.Yet,as a matter of fact,the prompts above indicates that there isn't an mpicc in my PC.Could anybody tell me what the hell the problem is. How can I fix it? Does "which mpicc" immediately before a failing configure show the correct executable? If it does, if you're setting the PATH manually, the only think I can think is that your shell environment in which the configure stuff gets executed is over-writing PATH in the dotfiles, not appending to it. Thus, you lose the effect of your PATH setting. So you could check for and/or fix that. Alternatively, try "./configure --blahblahblah MPICC=/path/to/mpicc" Another question, I am use a PC with dual-CPU, is it neccissary to install an MPI version? Will the difference between a gmx with or without a MPI in such a system be big enough to save our CPU time when implement a molecular dynamics? My system may contains about 1 or more atoms. Yes. MPI is the only way you can derive any advantage, which will be considerable. 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] mpi problem during installation
Itamar Kass wrote: HI all, I am trying to compile GROMACS 4.0.5 on my mac (10.5) using './configure --enable-mpi --disable-float --with-fft=no && make -j2 && make install'. I installed on the system lam 7.0.6 './configure && make && make install'. The error message I get is: mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -std=gnu99 -framework Accelerate -o grompp grompp.o ./.libs/libgmxpreprocess_mpi_d.a -L/usr/X11/lib ../mdlib/.libs/libmd_mpi_d.a /Users/ikass/Downloads/gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi_d.a ../gmxlib/.libs/libgmx_mpi_d.a /usr/lib/libxml2.dylib -lpthread -lz -licucore -lm /usr/X11/lib/libSM.6.0.0.dylib /usr/X11/lib/libICE.6.3.0.dylib /usr/X11/lib/libX11.6.2.0.dylib /usr/X11/lib/libXau.6.0.0.dylib /usr/X11/lib/libXdmcp.6.0.0.dylib Undefined symbols: "_lam_mpi_sum", referenced from: _lam_mpi_sum$non_lazy_ptr in libgmx_mpi_d.a(network.o) _lam_mpi_sum$non_lazy_ptr in libmd_mpi_d.a(domdec.o) _lam_mpi_sum$non_lazy_ptr in libmd_mpi_d.a(gmx_wallcycle.o) _lam_mpi_sum$non_lazy_ptr in libmd_mpi_d.a(pme.o) "_lam_mpi_comm_world", referenced from: _lam_mpi_comm_world$non_lazy_ptr in libgmx_mpi_d.a(network.o) _lam_mpi_comm_world$non_lazy_ptr in libgmx_mpi_d.a(main.o) "_lam_mpi_float", referenced from: _lam_mpi_float$non_lazy_ptr in libgmx_mpi_d.a(network.o) "_lam_mpi_double", referenced from: _lam_mpi_double$non_lazy_ptr in libgmx_mpi_d.a(network.o) _lam_mpi_double$non_lazy_ptr in libmd_mpi_d.a(partdec.o) _lam_mpi_double$non_lazy_ptr in libmd_mpi_d.a(gmx_wallcycle.o) _lam_mpi_double$non_lazy_ptr in libmd_mpi_d.a(pme.o) _lam_mpi_double$non_lazy_ptr in libmd_mpi_d.a(gmx_parallel_3dfft.o) "_lam_mpi_byte", referenced from: _lam_mpi_byte$non_lazy_ptr in libgmx_mpi_d.a(network.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(partdec.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(domdec.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(domdec_network.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(pme_pp.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(sim_util.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(pme.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(stat.o) "_lam_mpi_int", referenced from: _lam_mpi_int$non_lazy_ptr in libgmx_mpi_d.a(network.o) _lam_mpi_int$non_lazy_ptr in libmd_mpi_d.a(domdec.o) _lam_mpi_int$non_lazy_ptr in libmd_mpi_d.a(pme.o) mpicc tends to be a wrapper script that calls another compiler with the right libraries to compile MPI code for your system. If you had another MPI library installed, then things might get confused. Try "mpicc -h" or something to get some diagnostic information. You might try to invoke its verbose mode, or to get it to report what libraries it's trying to 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mpi problem
Hi, I fixed this problem on my login node on the cluster I'm using by getting the libXm.so.3 file from another machine and copying it to /home/bruce/lib/libXm.so.3. After that I could run GROMACS without re-compiling. (At least it stops the complaints about the missing library and lets you run jobs - I haven't tried the X interfaces to the programs though) Cheers, Bruce Quoting [EMAIL PROTECTED]: Date: Mon, 20 Mar 2006 22:44:30 +0800 From: Yang Ye <[EMAIL PROTECTED]> Subject: Re: [gmx-users] mpi problem To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=GB2312 Check your Linux's rpm resipository for a package containing this file. The best way of avoiding this could be using -without-x for Gromacs' configure. Yang Ye Rongliang Wu wrote: hello all, i've got a problem whem i intend to run a parallel mdrun, when i met with such error: error while loading shared libraries: libXm.so.3: cannot open shared object file: No such file or directory what's the problem and mpi is LAM -- Rongliang Wu 2006-03-20 ___ 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 This message was sent using IMP, the Internet Messaging Program. ___ 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] mpi problem
Check your Linux's rpm resipository for a package containing this file. The best way of avoiding this could be using -without-x for Gromacs' configure. Yang Ye Rongliang Wu wrote: > hello all, > i've got a problem whem i intend to run a parallel mdrun, when i met with > such error: > > error while loading shared libraries: libXm.so.3: cannot open shared object > file: No such file or directory > > what's the problem and mpi is LAM > > -- > Rongliang Wu > 2006-03-20 > > > ___ > 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 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] mpi problem
Hi, Sounds like you compiled on a frontend that has X11 installed, but the nodes you are running on don't. X11 is usually only available as a dynamic library (i.e., you can't compile it statically), so disable X11 support instead with ./configure --without-x (+ your current options) Cheers, Erik On Mar 20, 2006, at 12:57 PM, Rongliang Wu wrote: hello all, i've got a problem whem i intend to run a parallel mdrun, when i met with such error: error while loading shared libraries: libXm.so.3: cannot open shared object file: No such file or directory what's the problem and mpi is LAM -- Rongliang Wu 2006-03-20 ___ 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 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
