[Dock-fans] Errors encountered while make test-nu parallel

Scott Brozell sbrozell at rci.rutgers.edu
Wed Jun 8 23:53:50 PDT 2016


Hi,

On Wed, Jun 08, 2016 at 07:24:48PM -0700, Thanh Le wrote:
> The errors I encounter while installing dock6 gnu parallel:
> Processing parallel dock6 test mpi
> /bin/mpirun -np 2 ../../../bin/dock6.mpi -i mpi.dockin -o mpi.dockmpiout 
 ^^^^^^^^^^^^

> make[3]: /bin/mpirun: No such file or directory
> 
> my gne parallel: 
> MPICH_HOME=     /usr/local/Cellar/mpich/3.2_1
  ^^^^^^^^^^^

> CC=          gcc
> CXX=         $(MPICH_HOME)/bin/mpicxx
> CFLAGS=      -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I$(MPICH_HOME)/include -O2
> FC=          gfortran
> FFLAGS=      -O2 -fno-automatic -fno-second-underscore
> LIBS=        -lm
> LINK_WITHOUT_FORTRAN_MAIN=
> LOAD=        $(MPICH_HOME)/bin/mpicxx
> DOCK_SUFFIX= .mpi
> 
> I have no idea why I keep getting the errors listed above during make test.

Why is MPICH_HOME defined inside the config.h file ?
This does not define it as an environment variable.

You need to define the MPICH_HOME environment variable.
Eg, at the command line for sh type shells enter:
export MPICH_HOME=/usr/local/Cellar/mpich/3.2_1
or for csh type shells enter:
setenv MPICH_HOME /usr/local/Cellar/mpich/3.2_1
See
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#parallelinstallation
"Once MPI is installed, define the environment variable MPICH_HOME to the top level MPICH2 directory"

> Also, I would like to know what what mpi command is to run flx.in
> my path to dock6 file is
> /Users/thanhle/desktop/dock7/bin

See 
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#paralleldock

Why is your dock6 called dock7 ?
This is a recipe for confusion.

scott



More information about the Dock-fans mailing list