[gmx-users] Can't remove libpthreads from the link

David spoel at xray.bmc.uu.se
Mon Mar 14 21:56:45 CET 2005


On Mon, 2005-03-14 at 17:20 -0300, Paolo Victor wrote:
> Matt,
> 
> I've got the same problem with the lpthread lib linking. Did you find a solution?
> 
take out X windows and motif
> Thanks in advance,
> Paolo Victor
> 
> 
> >/ GMX-User List,
> />/ 
> />/ I am attempting to install Gromacs-3.2.1 on a Scyld 29-CZ4 Linux distribution. 
> />/ The Scyld OS has a problem doing a remote execute on an program that has the 
> />/ pthreads library linked in (regardless of the program actually using the 
> />/ pthreads calls). Consequently, I am trying to remove the pthreads library 
> />/ completely from the link.
> /try starting from scratch: remove your whole gromacs tree and untar a
> new one.
> >/ 
> />/ I start the gromacs build with the following command....
> />/ >>./configure --disable-threads --enable-mpi
> />/ 
> />/ However, when I do search for the pthreads library in the src Makefiles I get 
> />/ the following output
> />/ >>grep -R -e"lpthread" src/*
> />/ src/contrib/Makefile:LIBS =  -L/usr/X11R6/lib64 -lnsl -lsrfftw_mpi -lsfftw_mpi 
> />/ -lsrfftw -lsfftw -lm  -lXm -lXt  -lSM -lICE -lXext -lXp -lX11  -lxml2 -lz 
> />/ -lpthread -lm
> />/ src/gmxlib/Makefile:LIBS =  -L/usr/X11R6/lib64 -lnsl -lsrfftw_mpi -lsfftw_mpi 
> />/ -lsrfftw -lsfftw -lm  -lXm -lXt  -lSM -lICE -lXext -lXp -lX11  -lxml2 -lz 
> />/ -lpthread -lm 
> />/ .... (more of the same)......
> />/ 
> />/ And when I do a symbolic link analysis on the src/kernel/mdrun executable I 
> />/ get the following.....
> />/ >>make
> />/ >>cd src/kernel
> />/ >>ldd mdrun 
> />/         libnsl.so.1 => /lib64/libnsl.so.1 (0x0000002a9566b000)
> />/         libsrfftw_mpi.so.2 => /usr/local/lib/libsrfftw_mpi.so.2 
> />/ (0x0000002a95781000)
> />/         libsfftw_mpi.so.2 => /usr/local/lib/libsfftw_mpi.so.2 
> />/ (0x0000002a95883000)
> />/         libsrfftw.so.2 => /usr/local/lib/libsrfftw.so.2 (0x0000002a9598a000)
> />/         libsfftw.so.2 => /usr/local/lib/libsfftw.so.2 (0x0000002a95ab9000)
> />/         libXm.so.3 => /usr/X11R6/lib64/libXm.so.3 (0x0000002a95bf2000)
> />/         libXt.so.6 => /usr/X11R6/lib64/libXt.so.6 (0x0000002a95f8f000)
> />/         libSM.so.6 => /usr/X11R6/lib64/libSM.so.6 (0x0000002a960ef000)
> />/         libICE.so.6 => /usr/X11R6/lib64/libICE.so.6 (0x0000002a961f9000)
> />/         libXext.so.6 => /usr/X11R6/lib64/libXext.so.6 (0x0000002a96312000)
> />/         libXp.so.6 => /usr/X11R6/lib64/libXp.so.6 (0x0000002a96423000)
> />/         libX11.so.6 => /usr/X11R6/lib64/libX11.so.6 (0x0000002a9652b000)
> />/         libxml2.so.2 => /usr/lib64/libxml2.so.2 (0x0000002a96706000)
> />/         libz.so.1 => /usr/lib64/libz.so.1 (0x0000002a96925000)
> />/         libpthread.so.0 => /lib64/libpthread.so.0 (0x0000002a96a33000)
> />/         libm.so.6 => /lib64/libm.so.6 (0x0000002a96bc7000)
> />/         libmpich-gnu.so.1 => /usr/lib64/MPICH/p4/gnu/libmpich-gnu.so.1 
> />/ (0x0000002a96d4f000)
> />/         libbproc.so.2 => /usr/lib64/libbproc.so.2 (0x0000002a96f10000)
> />/         libc.so.6 => /lib64/libc.so.6 (0x0000002a97014000)
> />/         libXmu.so.6 => /usr/X11R6/lib64/libXmu.so.6 (0x0000002a97259000)
> />/         libdl.so.2 => /lib64/libdl.so.2 (0x0000002a97372000)
> />/         /lib64/ld-linux-x86-64.so.2 => /lib64/ld-linux-x86-64.so.2 
> />/ (0x0000002a95556000)
> />/         libbeomap.so.0.1 => /usr/lib64/libbeomap.so.0.1 (0x0000002a97475000)
> />/         libbpsh.so.0 => /usr/lib64/libbpsh.so.0 (0x0000002a97578000)
> />/         libbeostat.so.0 => /usr/lib64/libbeostat.so.0 (0x0000002a9767b000)
> />/ 
> />/ If I attempt to manually remove the -lpthread switch from all the make files 
> />/ and recompile/link I get....
> />/ >>some command to remove all -lpthread from Makefiles
> />/ >>make clean
> />/ >>make
> />/ >>cd src/kernel
> />/ >>ldd mdrun
> />/         libnsl.so.1 => /lib64/libnsl.so.1 (0x0000002a9566b000)
> />/         libsrfftw_mpi.so.2 => /usr/local/lib/libsrfftw_mpi.so.2 
> />/ (0x0000002a95781000)
> />/         libsfftw_mpi.so.2 => /usr/local/lib/libsfftw_mpi.so.2 
> />/ (0x0000002a95883000)
> />/         libsrfftw.so.2 => /usr/local/lib/libsrfftw.so.2 (0x0000002a9598a000)
> />/         libsfftw.so.2 => /usr/local/lib/libsfftw.so.2 (0x0000002a95ab9000)
> />/         libXm.so.3 => /usr/X11R6/lib64/libXm.so.3 (0x0000002a95bf2000)
> />/         libXt.so.6 => /usr/X11R6/lib64/libXt.so.6 (0x0000002a95f8f000)
> />/         libSM.so.6 => /usr/X11R6/lib64/libSM.so.6 (0x0000002a960ef000)
> />/         libICE.so.6 => /usr/X11R6/lib64/libICE.so.6 (0x0000002a961f9000)
> />/         libXext.so.6 => /usr/X11R6/lib64/libXext.so.6 (0x0000002a96312000)
> />/         libXp.so.6 => /usr/X11R6/lib64/libXp.so.6 (0x0000002a96423000)
> />/         libX11.so.6 => /usr/X11R6/lib64/libX11.so.6 (0x0000002a9652b000)
> />/         libxml2.so.2 => /usr/lib64/libxml2.so.2 (0x0000002a96706000)
> />/         libz.so.1 => /usr/lib64/libz.so.1 (0x0000002a96925000)
> />/         libm.so.6 => /lib64/libm.so.6 (0x0000002a96a33000)
> />/         libmpich-gnu.so.1 => /usr/lib64/MPICH/p4/gnu/libmpich-gnu.so.1 
> />/ (0x0000002a96bbb000)
> />/         libbproc.so.2 => /usr/lib64/libbproc.so.2 (0x0000002a96d7c000)
> />/         libc.so.6 => /lib64/libc.so.6 (0x0000002a96e80000)
> />/         libXmu.so.6 => /usr/X11R6/lib64/libXmu.so.6 (0x0000002a970c5000)
> />/         libdl.so.2 => /lib64/libdl.so.2 (0x0000002a971de000)
> />/         libpthread.so.0 => /lib64/libpthread.so.0 (0x0000002a972e1000)
> />/         libbeomap.so.0.1 => /usr/lib64/libbeomap.so.0.1 (0x0000002a97475000)
> />/         libbpsh.so.0 => /usr/lib64/libbpsh.so.0 (0x0000002a97578000)
> />/         libbeostat.so.0 => /usr/lib64/libbeostat.so.0 (0x0000002a9767b000)
> />/         /lib64/ld-linux-x86-64.so.2 => /lib64/ld-linux-x86-64.so.2 
> />/ (0x0000002a95556000)
> />/ 
> />/ Unfortunately, pthreads is still being linked in. 
> />/ 
> />/ Do you know of a way to completely remove this from the link?
> />/ 
> />/ Thanks,
> />/ Matt McMullen
> />/ _______________________________________________
> />/ gmx-users mailing list
> />/ gmx-users at gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users>
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> /
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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