[gmx-users] Problems installing GMX 4.0 RC4

[Justin A. Lemkul]

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

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