How to compile DOCK

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compiling dock3.8

Note- not every machine will have the prerequisite development libraries installed to compile DOCK fortran code. It is best to log into our "psi" machine, which is known to have the prerequisite libraries. Note: git will not work from psi, so you will need to have the code you would like to compile accessible via the NFS.

 ssh $USER@psi

Wynton development nodes are also a good place to compile with gfortran. For PGF you will always need to log into our psi machine.

gfortran instructions

gfortran is a widely available compiler that is preinstalled on all lab machines. In order to compile with gfortran, start from the base directory of DOCK and follow these instructions:

 cd ucsfdock/docking/DOCK/src/libfgz
 COMPILER=gfortran make
 cd ../i386
 COMPILER=gfortran make

You should now have a bunch of .o object files as well as a dock64 executable in the i386 directory. If you want to compile a debug build add DEBUG=1 before make, and if you want to compile for a different architecture prefix make with SIZE=[32|64]

If you mistakenly compile something (wrong compiler or the like) you can clean up the files produced from compilation with "make clean". Don't worry about the error messages you may get from this, something is a little fishy with our makefile.

It may be necessary to run make twice due to an odd error with the version.f file.

pgf instructions

PGF or the Portland Group compiler is the premium option for fortran compilation. In order to compile with pgf you must log onto the psi machine, where the license and installation is located.

 ssh $USER@psi

Set up the compilation environment through the following script:

 bash # if you are not already on bash
 export PATH=/nfs/soft/pgi/current/linux86-64/12.10/bin:$PATH
 source /nfs/home/tbalius/zzz.virtualenvs/virtualenv-1.9.1/myVEonGimel/bin/activate
 source /nfs/soft/pgi/env.sh

The instructions to compile are identical to those for gfortran, the only difference being you need to set COMPILER=pgf, e.g

 cd ucsfdock/docking/DOCK/src/libfgz
 COMPILER=pgf make
 cd ../i386
 COMPILER=pgf make

You can add DEBUG, SIZE etc. options just like gfortran.

Sometimes there is an odd error with the licensing server that causes compilation to fail. I don't remember exactly I fixed this in the past, but I believe it had to do with restarting the license service via systemctl.

It may be necessary to run make twice due to an odd error with the version.f file.

compiling dock3.7

 1. log into psi (portland fortran compiler is on psi)
 2. export PATH=/nfs/soft/pgi/current/linux86-64/12.10/bin:$PATH	
 3. source Trent's virual environment (source /nfs/home/tbalius/zzz.virtualenvs/virtualenv-1.9.1/myVEonGimel/bin/activate)
 4. source /nfs/soft/pgi/env.csh

DOCK 3.7

Frist you need the source code:

  • lab members and other developers may check out dock from Github
  • others can request the distrabution here [1]

compiling dock

To compile DOCK go to path/DOCK/src/i386

make
make DEBUG=1
make SIZE=32 [64]
make clean

Note:

  • To compile with portland group compilers
    • go to a machine were pgf linsence is installed (sgehead1 or psi).
  • To add a file for compilation, add the xxxx.f file to path/DOCK/src/ and add xxxx.o to i386/Makefile object list.

debuging dock

Debugging :

 pgdbg  path/DOCK/src/i386/dock_prof64

profiling dock

Profiling:

make pgprofile
less pgprof.out
pgprof - opens a GUI profiler that interprets pgprof.out !

you may also do the following:

make dock_prof64
cd /dir/test 
/dockdir/dock_prof64 INDOCK
less pgprof.out
make gmon.out
less gmon.out
make gprofile
less gprofile.txt

DOCK 3.5.54

This is for the Shoichet Lab local version of DOCK 3.5.54 trunk.

Checking out the source files

Commands:

csh
mkdir /where/to/put
cd /where/to/put
svn checkout file:///raid4/svn/dock
svn checkout file:///raid4/svn/libfgz

Compiling the program on our cluster

First, you need to set the path to the PGF compiler by adding this line to your .login file (at the end):

setenv DOCK_BASE ~xyz/dockenv
echo DOCK_BASE set to $DOCK_BASE.
source $DOCK_BASE/etc/login

When you login to sgehead now, you should see the "Enabling pgf compiler" message

Commands:

ssh sgehead
cd /where/to/put/libfgz/trunk
make

Since we still have some 32bit computers, you'll also want to do

make SIZE=32

before leaving the libfgz branch and going to DOCK:

cd ../../dock/trunk/i386
make

This makes the 64 bit version. Some options:

make SIZE=32

Makes the 32bit version, useful for running on the cluster since some machines are older.

make DEBUG=1 

Makes a debug version that will report line numbers of errors and is usable with pgdbg (the Portland Group Debugger), which is useful when writing code but is 10x (or more) slower.

Compiling the program on the shared QB3 cluster

On one of the compilation nodes on the shared QB3 cluster (optint1 or optint2):

ssh optint2
cd /where/to/put/libfgz/trunk
cp Makefile Makefile.old
modify Makefile:
 uncomment the following:
 FC = ifort -O3
 CC = icc -O3
make
cd ../../dock/trunk/i386
cp Makefile Makefile.old
modify Makefile
 uncomment the following:
 F77 = ifort
 FFLAGS = -O3 -convert big_endian
make dock