Ptraj

Compilation on Bluegene

Download the latest ptraj source code from Cheatham Lab Untar and gzip the source code into it's own folder. Note that the tar file does not make it's own folder. Try to compile with 'make' Compilation will halt because of the error:

/usr/bin/ld: skipping incompatible netcdf/src/libsrc/libnetcdf.a when searching for -lnetcdf
/usr/bin/ld: cannot find -lnetcdf
collect2: ld returned 1 exit status
make: *** [rdparm] Error 1

Go inside the netcdf/src folder. The problem occurs because netcdf gets compiled with the IBM xlC compiler, but then tries to use gcc ld during the linking phase. To solve this, we will compile netcdf with the gcc compiler.

'make clean' to delete all netcdf object files
'./configure CC=gcc CXX=g++ FC=f77' to use GNU compilers
'make' to compile netcdf successfully
Go back to the ptraj folder. cd ../.. should do it
Use 'make'. Do not make clean as it will delete the netcdf compile
You should get a ptraj and rdparm binary!