Re: [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu"

From: Tru Huynh <tru.pasteur.fr>
Date: Fri, 5 Oct 2012 09:42:03 +0200

On Thu, Oct 04, 2012 at 02:42:50PM -0400, Jason Swails wrote:
> On Thu, Oct 4, 2012 at 1:21 PM, Su, Shiquan <ssu2.utk.edu> wrote:
>
...
>
> I can try to switch environments over to GNU, but it may take me a little
> bit to do so.

It's a openmpi "feature" :)

I had to manually add to PMEMD_CU_LIBS in config.h the -lmpi_cxx flag:

PMEMD_CU_LIBS=./cuda/cuda.a -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib -lcurand -lcufft -lcudart
changed to:
PMEMD_CU_LIBS=./cuda/cuda.a -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib -lcurand -lcufft -lcudart -lmpi_cxx


you might also have a small issue with the netcdf builds for gcc44/gfortran44 on CentOS-5

1) the AmberTools/src/configure2 is not matching gfortran44 as gfortran:

[tru.sillage src]$ diff -uNr configure2.ori configure2
--- configure2.ori 2012-09-10 10:30:10.000000000 +0200
+++ configure2 2012-09-14 09:03:32.000000000 +0200
.@ -615,18 +615,19 @@
       if [ "$mpi" = 'yes' ]; then
         ld=' mpif90 '
       else
- ld=' gfortran '
+ ld=' gfortran44 '
       fi
     fi
     flibs_arch="-lgfortran -w"
     flibsf_arch=
- cc=gcc
+ cc=gcc44
     cflags=
     ambercflags=""
- cplusplus=g++
+ cplusplus=g++44
     cxxflags=
     ambercxxflags=""
- fc=gfortran
+ fc=gfortran44
+# fix also netcdf/src/configure to recognize gfortran|gfortran44
     fflags=
     staticflag='-static'
     
.@ -1733,7 +1734,7 @@
           pgi*)
               ./configure \
                   FC="$fc" F90="$fc" \
- FFLAGS="$ldflags $foptflags" FCFLAGS="$ldflags $foptflags" \
+ FFLAGS="$fflags $foptflags" FCFLAGS="$fflags $foptflags" \
                   F90FLAGS="$ldflags $foptflags" \
                   CPPFLAGS="-DNDEBUG -DpgiFortran" \
                   CC="$cc" CFLAGS="$cflags $cnooptflags" \
.@ -1744,7 +1745,7 @@
           *)
               ./configure \
                   FC="$fc" F90="$fc" \
- FFLAGS="$ldflags $foptflags" FCFLAGS="$ldflags $foptflags" \
+ FFLAGS="$fflags $foptflags" FCFLAGS="$fflags $foptflags" \
                   F90FLAGS="$ldflags $foptflags" \
                   CPPFLAGS="-DNDEBUG" \
                   CC="$cc" CFLAGS="$cflags $cnooptflags" \

2) the netcdf configure is not matching gfortran44 as gfortran:
[tru.sillage gcc44]$ diff -uN AmberTools/src/netcdf/src/configure.ori AmberTools/src/netcdf/src/configure
--- AmberTools/src/netcdf/src/configure.ori 2012-10-05 09:38:57.263609997 +0200
+++ AmberTools/src/netcdf/src/configure 2012-09-14 09:02:19.000000000 +0200
.@ -21829,7 +21829,7 @@
 _ACEOF
 
                ;;
- gfortran)
+ gfortran|gfortran44)
                # Support for gfortran ver > 4.1 backported from snapshot
                 if (gfortran --version | grep "(GCC) 4.1." || gfortran --version | grep "(GCC) 4.0."); then


$ module av amber/12
amber/12/20120910/openmpi-1.6.1/cuda-4.2.9/gcc-4.6.2-gmp-4.3.2-mpfr-3.1.0-mpc-0.8.2
amber/12/20120910/openmpi-1.6.1/cuda-4.2.9/gcc44
amber/12/20120910/openmpi-1.6.1/cuda-4.2.9/gnu
amber/12/20120910/openmpi-1.6.1/cuda-4.2.9/intel-12-2011.8.273
amber/12/20120910/openmpi-1.6.1/gcc-4.6.2-gmp-4.3.2-mpfr-3.1.0-mpc-0.8.2
amber/12/20120910/openmpi-1.6.1/gcc44
amber/12/20120910/openmpi-1.6.1/gnu
amber/12/20120910/openmpi-1.6.1/intel-12-2011.8.273
amber/12/20120910/serial/cuda-4.2.9/gcc-4.6.2-gmp-4.3.2-mpfr-3.1.0-mpc-0.8.2
amber/12/20120910/serial/cuda-4.2.9/gcc44
amber/12/20120910/serial/cuda-4.2.9/gnu
amber/12/20120910/serial/cuda-4.2.9/intel-12-2011.8.273
amber/12/20120910/serial/gcc-4.6.2-gmp-4.3.2-mpfr-3.1.0-mpc-0.8.2
amber/12/20120910/serial/gcc44
amber/12/20120910/serial/gnu
amber/12/20120910/serial/intel-12-2011.8.273
Cheers,

Tru
-- 
Dr Tru Huynh          | http://www.pasteur.fr/recherche/unites/Binfs/
mailto:tru.pasteur.fr | tel/fax +33 1 45 68 87 37/19
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France  
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Received on Fri Oct 05 2012 - 01:00:03 PDT
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