[gmx-users] Cant remove libpthreads from the link

David spoel at xray.bmc.uu.se
Fri Mar 4 18:56:27 CET 2005


On Fri, 2005-03-04 at 09:40 -0800, Matt McMullen wrote:
> 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
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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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