[gmx-users] Problems installing GMX 4.0 RC4

David van der Spoel spoel at xray.bmc.uu.se
Thu Oct 9 14:38:04 CEST 2008 

Justin A. Lemkul wrote:
> 
> 
> David van der Spoel wrote:
>> Justin A. Lemkul wrote:
>>>
>>> To follow up just a bit more - it appears that this problem is 
>>> isolated to the PowerPC architecture.  I can compile and install RC4 
>>> on my own laptop (a recent Intel Mac) with no problems.
>> Not sure that I can help, but Erik recently fixed a bug report related 
>> to CPU detection on Macs. Is your cluster running MacOS or Linux?
> 
> We are running Mac OS X 10.3.9.
If you still have the previous RC3 around, you can try to use the 
configure script that comes with that one. There have been quite a few 
apple related changes in between these versions.

> 
> -Justin
> 
>>>
>>> -Justin
>>>
>>> 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
>>>>>
>>>>
>>>
>>
>>
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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