Amber on Seawulf (compilation)

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compiling Amber9

Follow the steps in the INSTALL file.

At step 5, edit config.h by change g95 to gfortrain.

The following lib file is not found by the compiler 

 /usr/include/X11/extensions/shape.h

I copied the following dir from another machine: 

 /usr/include/X11/extensions

and put it in my home dir in: 

 ~/usr/include/X11/extensions

I modified the files changing the reported line number: 

/nfs/user03/tbalius/amber9/src/leap/src/Xmu/ShapeWidg.c line: 27 
/nfs/user03/tbalius/amber9/src/leap/src/Xraw/Logo.c     line: 26
/nfs/user03/tbalius/amber9/src/leap/src/Xraw/Mailbox.c  line: 64 

from:
#include <X11/extensions/shape.h>
to:
#include </nfs/user03/tbalius/usr/include/X11/extensions/shape.h>

instead we should have 

 /usr/include/X11/extensions/shape.h  	 x11proto-xext-dev

installed.


I get the following Error: 

/usr/bin/ld: cannot find -lXext

possible solutions: 


cd /usr/lib
ln -s ./libXext.so.6.4.0 ./libXext.so

instead I did the following: 

cd ~/user
mkdir lib
ln -s /usr/lib/libXext.so.6.4.0 libXext.so
cd ../
ln -s lib lib64
ln -s lib lib32

Then I changed the following file at the specified line: 

 amber9/src/leap/src/leap/Makefile  line:117

from: 

../Xmu/libXmu.a $(XLIBS) -lXt -lXext -lSM -lICE -lX11 $(LM) -lpthread

to: 

../Xmu/libXmu.a -L/nfs/user03/tbalius/usr/lib/ -lXext -L/usr/lib/ -lXt -lSM -lICE -lX11 -lm -lpthread

MAKE PARALLEL 

./configure -mpich2 -p4 gfortran
AMBERHOME is set to /nfs/user03/tbalius/amber9
Setting up Amber configuration file for architecture: gfortran
Using parallel communications library: mpich2
MPI_HOME is set to /nfs/user03/tbalius/mpich2-install
 ./configure: line 314: /nfs/user03/tbalius/mpich2-install/bin/mpif90: No such file or directory
The MKL_HOME environment variable is not defined.

The configuration file, config.h, was successfully created.


Because of the bold error, we change configure file at line 313:

from: 

    loadlib=`$MPI_HOME/bin/mpif90 -show | perl -p -e 's/(-[lL]\S+\s)|\S+\s/$1/g'`

to: 

    loadlib=`$MPI_HOME/bin/mpif77 -show | perl -p -e 's/(-[lL]\S+\s)|\S+\s/$1/g'`

compiling Amber10

while making amber10 tools I get the following error: 

  ShapeWidg.c:27:34: error: X11/extensions/shape.h: No such file or directory

Like above changed the same files:

From: 

Xmu/ShapeWidg.c:#include <X11/extensions/shape.h>
Xraw/Logo.c:#include <X11/extensions/shape.h>
Xraw/Mailbox.c:#include <X11/extensions/shape.h>

To: 

Xmu/ShapeWidg.c:#include </nfs/user03/tbalius/usr/include/X11/extensions/shape.h>
Xraw/Logo.c:#include </nfs/user03/tbalius/usr/include/X11/extensions/shape.h>
Xraw/Mailbox.c:#include </nfs/user03/tbalius/usr/include/X11/extensions/shape.h>


Next, I get the same error as in amber9. 

 /usr/bin/ld: cannot find -lXext

During linking.

I change the following file at the specified line: 

amber10/src/leap/src/leap/Makefile at line 114
from 
    ../Xmu/libXmu.a $(XLIBS) -lXt -lXext -lSM -lICE -lX11 -lXau -lXdmcp $(LM) -lpthread
to
    ../Xmu/libXmu.a $(XLIBS) -lXt -lSM -lICE -lX11 -lXau -lXdmcp -L/nfs/user03/tbalius/usr/lib -lXext $(LM) -lpthread


Problem with testing amber tools:

Running test to compute GB Newton-Raphson and normal modes: 

/nfs/user03/tbalius/amber10/lib/libnab.a(newton.o): In function `newton':
newton.c:(.text+0xba8): undefined reference to `assert'
/nfs/user03/tbalius/amber10/lib/libnab.a(nmode.o): In function `nmode':
nmode.c:(.text+0x511e): undefined reference to `assert'
collect2: ld returned 1 exit status
cc failed! 
make[1]: *** [asp_test] Error 1
make[1]: Leaving directory `/nfs/user03/tbalius/amber10/test/nab'
make: *** [test.nab] Error 2

every thing else ran.

configure amber with gfortran 

./configure_amber gfortran

Because I am compiling a cheek out from the CVS tree I had to modify 4 files in the source code and cp one file (qmmm_module.mod ) to a different dir

when running 

 make serial

First is seems that the following file need to be placed to the following dir and it is not being copied there:

after: 

make serial 
cp sander/qmmm_module.mod dcqtp/mod/ 
make serial


I get the following error: 

 gfortran: ../../sander: linker input file unused because linking not done
 gfortran -c -O1 -fno-automatic   -ffree-form ../../sander -I../src/include -DHAS_LAPACK -DQMMM -o ../obj/freq_qmmm.o ../src/freq/freq.F90
 ../src/freq/freq.F90:11.38:

    use qmmm_module, only: qmmm_struct, qmmm_div
                                    1
 Error: Symbol 'qmmm_div' referenced at (1) not found in module 'qmmm_module'

../src/freq/freq.F90:38.26: 

   dimension dcl(3,qmmm_div%ntotatm+qmmm_struct%nlink)
                        1
 Error: Expected another dimension in array declaration at (1)
 make[3]: *** [../obj/freq_qmmm.o] Error 1
 make[3]: Leaving directory `/nfs/user03/tbalius/amber10/src/dcqtp/mod'
 make[2]: *** [libdivcon.a] Error 2
 make[2]: Leaving directory `/nfs/user03/tbalius/amber10/src/dcqtp'
 make[1]: *** [divcon] Error 2
 make[1]: Leaving directory `/nfs/user03/tbalius/amber10/src/sander'
 make: *** [serial] Error 2


change the following lines: 

1)amber10/src/dcqtp/src/freq/freq.F90:11:
  use qmmm_module, only: qmmm_struct, qmmm_div
amber10/src/dcqtp/src/freq/freq.F90:38:
 dimension dcl(3,qmmm_div%ntotatm+qmmm_struct%nlink)
2)amber10/src/dcqtp/src/mem/allocateScrfVars.F90:10:
 use qmmm_module, only : qmmm_struct, qmmm_div
amber10/src/dcqtp/src/mem/allocateScrfVars.F90:45:
 allocate (atarea(qmmm_div%ntotatm+qmmm_struct%nlink), stat=ierror)
3)amber10/src/dcqtp/src/pb/pbsolver.F90:36:
 use qmmm_module, only : qmmm_struct, qmmm_nml, qmmm_div
amber10/src/dcqtp/src/pb/pbsolver.F90:73:
       allocate(charges(qmmm_div%ntotatm+qmmm_struct%nlink),stat=ier)
amber10/src/dcqtp/src/pb/pbsolver.F90:123:
             do i=1,qmmm_div%ntotatm+qmmm_struct%nlink
amber10/src/dcqtp/src/pb/pbsolver.F90:131:
                     call divpb(qmmm_div%ntotatm+qmmm_struct%nlink, &
amber10/src/dcqtp/src/pb/pbsolver.F90:133:
                     qmmm_div%all_atom_numbers, &
amber10/src/dcqtp/src/pb/pbsolver.F90:142:
            do i=1,qmmm_div%ntotatm+qmmm_struct%nlink
amber10/src/dcqtp/src/pb/pbsolver.F90:151:
                    do j=qmmm_div%ntotatm+qmmm_struct%nlink,i,-1
amber10/src/dcqtp/src/pb/pbsolver.F90:162:
                    do j=qmmm_div%ntotatm+qmmm_struct%nlink,i,-1
amber10/src/dcqtp/src/pb/pbsolver.F90:163:
                       temp = qmmm_div%all_atom_numbers(j-1)
amber10/src/dcqtp/src/pb/pbsolver.F90:164:
                       qmmm_div%all_atom_numbers(j)=temp
amber10/src/dcqtp/src/pb/pbsolver.F90:166:
                    qmmm_div%all_atom_numbers(i)=1
amber10/src/dcqtp/src/pb/pbsolver.F90:184:
            call divpb(qmmm_div%ntotatm+qmmm_struct%nlink, &
amber10/src/dcqtp/src/pb/pbsolver.F90:186:
                     qmmm_div%all_atom_numbers, &

for the frist occurence in every file remove qmmm_div; eg, change

from: 

use qmmm_module, only: qmmm_struct, qmmm_div

to: 

use qmmm_module, only: qmmm_struct

for other occurences change qmmm_div to qmmm_struct

To change this with ease do the following: 

 cd ${AMBERHOME}/src/dcqtp/src
 sed -i 's/qmmm_div/qmmm_struct/g' freq/freq.F90
 sed -i 's/qmmm_div/qmmm_struct/g' mem/allocateScrfVars.F90
 sed -i 's/qmmm_div/qmmm_struct/g' pb/pbsolver.F90

sed -i is for in place edits (meaning modifying the input file).

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