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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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