[gmx-users] Problems installing GMX 4.0 RC4

[Erik Lindahl]

Hi Justin,

This might be due to shared libraries, which I thought always worked  
on OS X :-)

Could you try with the option --disable-shared?

I guess the world still might not be ready for default shared  
libraries... in that case I'll disable it.

Cheers,

Erik

On Oct 9, 2008, at 4:36 AM, Justin A. Lemkul wrote:

>
> 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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