Amber on Seawulf (compilation)

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Revision as of 18:02, 10 December 2009 by Tbalius (talk | contribs) (compiling Amber10)
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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


I copied the following dir from another machine:


and put it in my home dir in:


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 

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

instead we should have

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


I get the following Error:

/usr/bin/ld: cannot find -lXext

possible solutions:

cd /usr/lib
ln -s ./ ./

instead I did the following:

cd ~/user
mkdir lib
ln -s /usr/lib/
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


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


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


./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:


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


    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:


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


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
    ../Xmu/libXmu.a $(XLIBS) -lXt -lXext -lSM -lICE -lX11 -lXau -lXdmcp $(LM) -lpthread
    ../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: *** [] Error 2

every thing else ran.

configure amber with gfortran

./configure_amber gfortran