A follow-up to my previous message: I've just compiled RC2 and RC3 to confirm
that nothing has changed within our system configuration; both RC2 and RC3
compile and install with no problems using the procedure in my previous message.
I am still faced with the fact that RC4 will not compile. Any ideas?
-Justin
Justin A. Lemkul wrote:
Hi,
I've been working to install the latest release candidate from Gromacs
4.0; I have installed RC1 and RC2 without any problems on our cluster.
We are running Mac OSX 10.3.9 on PowerPC nodes (G5 processors). My
installation process for installing mdrun is really pretty textbook:
./configure --program-suffix=_mpi --enable-mpi
make mdrun
make install-mdrun
This has always worked. With RC4, I get the following during
compilation (sorry, it's long):
ld: common symbols not allowed with MH_DYLIB output format with the
-multi_module option
ld: common symbols not allowed with MH_DYLIB output format with the
-multi_module option
//usr/bin/libtool: nfs/internal link edit command failedcompilers/
mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of common _MPIR_dtes
(size 4)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initutil.o) definition of
common _MPIR_errhandlers (size
4)/nfs/compilers/mpich-1.2.5/lib/libmpich.a(mpid_init.o) definition of
common _MPID_MyWorldRank (size 4)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(mpid_init.o) definition of
common _MPID_MyWorldSize (size
4)/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initutil.o) definition of
common _MPIR_fdtels (size 4)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initutil.o) definition of
common _MPIR_qels (size
4)/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initutil.o) definition of
common _MPIR_tid (size 4)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initutil.o) definition of
common _MPIR_topo_els (size 4)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(debugutil.o) definition of
common _MPIR_All_communicators (size 8)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(mpid_init.o) definition of
common _MPIR_rhandles (size
4)/nfs/compilers/mpich-1.2.5/lib/libmpich.a(mpid_init.o) definition of
common _MPIR_shandles (size 4)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(dreg.o) definition of common
_hpc_mem (size 4)/nfs/compilers/mpich-1.2.5/lib/libmpich.a(dreg.o)
definition of common _hpc_mem_size (size
4)/nfs/compilers/mpich-1.2.5/lib/libmpich.a(queue.o) definition of
common _MPID_recvs (size 16)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(initfutil.o) definition of
common _MPIR_I_2COMPLEX (size 104)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(initfutil.o) definition of
common _MPIR_I_2DCOMPLEX (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_2DOUBLE (size
104)/nfs/compilers/mpich-1.2.5/lib/libmpich.a(initfutil.o) definition of
common _MPIR_I_2DOUBLE_PRECISION (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_2FLOAT (size
104)/nfs/compilers/mpich-1.2.5/lib/libmpich.a(initfutil.o) definition of
common _MPIR_I_2INTEGER (size 104)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(initfutil.o) definition of
common _MPIR_I_2REAL (size
104)/nfs/compilers/mpich-1.2.5/lib/libmpich.a(initfutil.o) definition of
common _MPIR_I_COMPLEX (size 104)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(initfutil.o) definition of
common _MPIR_I_DCOMPLEX (size 104)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(initfutil.o) definition of
common _MPIR_I_DOUBLE_PRECISION (size 104)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(initfutil.o) definition of
common _MPIR_I_INTEGER (size 104)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(initfutil.o) definition of
common _MPIR_I_LOGICAL (size
104)/nfs/compilers/mpich-1.2.5/lib/libmpich.a(initfutil.o) definition of
common _MPIR_I_REAL (size 104)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(initfutil.o) definition of
common _MPIR_int1_dte (size
104)/nfs/compilers/mpich-1.2.5/lib/libmpich.a(initfutil.o) definition of
common _MPIR_int2_dte (size 104)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(initfutil.o) definition of
common _MPIR_int4_dte (size
104)/nfs/compilers/mpich-1.2.5/lib/libmpich.a(initfutil.o) definition of
common _MPIR_real4_dte (size 104)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(initfutil.o) definition of
common _MPIR_real8_dte (size
104)/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_2INT (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_BYTE (size
104)/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_CHAR (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_DOUBLE (size
104)/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_DOUBLE_INT (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_FLOAT (size
104)/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_FLOAT_INT (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_INT (size
104)/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_LB (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_LONG (size
104)/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_LONG_DOUBLE (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_LONG_DOUBLE_INT (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_LONG_INT (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_LONG_LONG_INT (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_PACKED (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_SHORT (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_SHORT_INT (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_UB (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_UCHAR (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_UINT (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_ULONG (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPIR_I_USHORT (size 104)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPI_DOUBLE_INT_var (size 16)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPI_FLOAT_INT_var (size 8)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPI_LONG_DOUBLE_INT_var (size 16)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPI_LONG_INT_var (size 8)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(initdte.o) definition of
common _MPI_SHORT_INT_var (size 8)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(util_hbt.o) definition of
common _MPIR_hbt_els (size 4)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(util_hbt.o) definition of
common _MPIR_hbts (size 4)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(global_ops.o) definition of
common _MPIR_Op_errno (size 4)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(debugutil.o) definition of
common _MPIR_debug_c (size 4)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(debugutil.o) definition of
common _MPIR_debug_cl (size 4)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(debugutil.o) definition of
common _MPIR_debug_q (size 4)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(debugutil.o) definition of
common _MPIR_debug_qel (size 4)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(debugutil.o) definition of
common _MPIR_debug_qh (size 4)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(debugutil.o) definition of
common _MPIR_debug_rh (size 4)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(debugutil.o) definition of
common _MPIR_debug_s (size 4)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(debugutil.o) definition of
common _MPIR_debug_sq (size 4)
/nfs/compilers/mpich-1.2.5/lib/libpmpich.a(debugutil.o) definition of
common _MPIR_debug_sqel (size 4)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(mpid_smpi.o) definition of
common _smpi (size 9252)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(viapriv.o) definition of
common _viadev (size 18492)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(dreg.o) definition of common
_dreg_free_list (size 4)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(dreg.o) definition of common
_dreg_table (size 262144)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(dreg.o) definition of common
_dreg_unused_list (size 4)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(dreg.o) definition of common
_dreg_unused_tail (size 4)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(mpid_smpi.o) definition of
common _smpi_shmem (size 4)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(initfcmn.o) definition of
common _mpipriv_ (size 36)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(viapriv.o) definition of
common _nullsbuffer (size 1)
/nfs/compilers/mpich-1.2.5/lib/libmpich.a(viapriv.o) definition of
common _nullrbuffer (size 1)
make[2]: *** [libgmx_mpi.la] Error 1
make[1]: *** [all-recursive] Error 1
Does anyone know how to solve this? We use gcc-3.3/mpicc-3.3 with
mpich-1.2.5; I have used these same compilers for all the Gromacs
installations on this cluster. If I can provide any additional
information, I'd be happy to do so.
Thanks for your attention.
-Justin
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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 list gmx-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
