[gmx-users] Problems installing GMX 4.0 RC4

[David van der Spoel]

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?
> 
> -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