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

[Paolo Victor]

Matt,

I've got the same problem with the lpthread lib linking. Did you find a solution?

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
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