[gmx-users] Problems installing GMX 4.0 RC4

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 9 13:36:24 CEST 2008 

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

========================================

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