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AMBER Archive (2007)Subject: RE: AMBER: amber9 compile problem
From: Ross Walker (ross_at_rosswalker.co.uk)
Hi Henk,
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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Henk Meij
Ross, with link in place
-Henk
[root_at_swallowtail src]# make clean
[root_at_swallowtail src]# ./configure -mpich ifort_x86_64
AMBERHOME is set to /share/apps/amber/9_ifort
Setting up Amber configuration file for architecture: ifort_x86_64
Using parallel communications library: mpich
MPI_HOME is set to /usr/local/topspin/mpi/mpich
MKL_HOME is set to /share/apps/intel/cmkl/9.1
Using MKL libraries from /share/apps/intel/cmkl/9.1/lib/em64t
The configuration file, config.h, was successfully created.
[root_at_swallowtail src]# which mpif90
/usr/local/topspin/mpi/mpich/bin/mpif90
[root_at_swallowtail src]# which ifort
/share/apps/intel/fce/9.1.043/bin/ifort
[root_at_swallowtail src]# make parallel
first error when compiling sander.MPI
IPO link: can not find -lmpif90_i
ifort: error: problem during multi-file optimization compilation (code 1)
so i changed config.h
#LOADLIB= -L/usr/local/topspin/mpi/mpich/lib -lmpichf90_i ...
LOADLIB= -L/usr/local/topspin/mpi/mpich/lib64 -lmpichf90_i ...
reran, and now have error
IPO link: can not find -lvapi
ifort: error: problem during multi-file optimization compilation (code 1)
[root_at_swallowtail src]# file /usr/local/topspin/lib64/libvapi.*
/usr/local/topspin/lib64/libvapi.a: current ar archive
/usr/local/topspin/lib64/libvapi.so: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
Hi Henk,
/\
| HPC Consultant and Staff Scientist |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.
_____
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Henk Meij
Ross, here it is.
1001 cd /share/apps/amber/
1002 mkdir 9_ifort
1003 cd 9_ifort/
1004 tar zxf /share/apps/src/amber9.tgz
1005 mv amber9/* .
1006 rmdir amber9/
1007 sh < /share/apps/src/amber9_bugfix.cmd
1008 cd src
1009 export PATH=/usr/local/topspin/mpi/mpich/bin:$PATH
1010 export MPI_HOME=/usr/local/topspin/mpi/mpich
1011 export AMBERHOME=/share/apps/amber/9_ifort
1012 export MKL_HOME=/share/apps/intel/cmkl/9.1
[root_at_swallowtail]# which mpif90.i
/usr/local/topspin/mpi/mpich/bin/mpif90.i
[root_at_swallowtail]# which ifort
/share/apps/intel/fce/9.1.043/bin/ifort
[root_at_swallowtail]# ./configure -mpich ifort_x86_64
AMBERHOME is set to /share/apps/amber/9_ifort
Setting up Amber configuration file for architecture: ifort_x86_64
Using parallel communications library: mpich
MPI_HOME is set to /usr/local/topspin/mpi/mpich
./configure: line 300: /usr/local/topspin/mpi/mpich/bin/mpif90: No such file or directory
MKL_HOME is set to /share/apps/intel/cmkl/9.1
Using MKL libraries from /share/apps/intel/cmkl/9.1/lib/em64t
"make parallel" yields an error when compiling
"ifort -FR -o sander.MPI evb_vars.o ..."
evb_init.o(.text+0x69e): In function `evb_init_':
: undefined reference to `mpi_bcast_'
-lots of these-
i've seen dac's fix for this but adding -fsecond-underscore does not fix the problem.
meaning i have to have clean source code for topspin and compile with -fno-secoond-underscore?
-Henk
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