[petsc-users] compiling code that uses Petsc and Sundials

[Sanjay Kharche]

Dear All

I would like to compile my code that uses Petsc and Sundials using a morph of the petsc makefile on my supercomputer. There are a few technical issues that I will appreciate your feedback on.

My code uses Petsc and Sundials. On my local machine, I installed Petsc with Sundials. The makefile examples I got allow me to compile my code which is a single file. I can see that -lsundials_cvode -lsundials_nvecserial -lsundials_nvecparallel are all there, as well as the blas lapack. Pasted below is my simple makefile and what happens when I make sk2d

Now I want to port my code to our local supercomputer, where I am not admin. The admin have installed petsc. I managed to compile and run the examples of that install - so it works on its own. This copy of petsc was not installed by connecting to Sundials. Therefore, I have installed sundials in my home directory. I tried to add the sundials paths in the makefile below at various locations (in fact, I could not work out where exactly to put the includes and libs!), but I could not get my code to compile. Any suggestions?

cheers
Sanjay

Local computer makefile:
 cat makefile 

include ${PETSC_DIR}/conf/variables
include ${PETSC_DIR}/conf/rules

sk2d: 	sk2d.o  chkopts
	-${CLINKER} -o sk2d sk2d.o  ${PETSC_TS_LIB} -lm -inline-calloc

veryclean:
	rm -rf *.dat *.vtk *.vts ex15 *.o sk2d *~

output of make sk2d:

make sk2d
/media/6c6201d2-4e2e-4b24-8d04-263b5bc06dfa/sanjay/petsc/linux-gnu-c-debug/bin/mpicc -o sk2d.o -c -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 -O0   -I/export2/sanjay/petsc/include -I/export2/sanjay/petsc/linux-gnu-c-debug/include -I/media/6c6201d2-4e2e-4b24-8d04-263b5bc06dfa/sanjay/petsc/linux-gnu-c-debug/include    `pwd`/sk2d.c
/export2/sanjay/mypetscProgs/Work/twod/sk2d.c: In function ‘main’:
/export2/sanjay/mypetscProgs/Work/twod/sk2d.c:112:24: warning: variable ‘usr_time’ set but not used [-Wunused-but-set-variable]
/export2/sanjay/mypetscProgs/Work/twod/sk2d.c:111:7: warning: unused variable ‘output’ [-Wunused-variable]
/export2/sanjay/mypetscProgs/Work/twod/sk2d.c:101:72: warning: unused variable ‘usr_nbs’ [-Wunused-variable]
/media/6c6201d2-4e2e-4b24-8d04-263b5bc06dfa/sanjay/petsc/linux-gnu-c-debug/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 -O0  -o sk2d sk2d.o  -Wl,-rpath,/export2/sanjay/petsc/linux-gnu-c-debug/lib -L/export2/sanjay/petsc/linux-gnu-c-debug/lib  -lpetsc -Wl,-rpath,/media/6c6201d2-4e2e-4b24-8d04-263b5bc06dfa/sanjay/petsc/linux-gnu-c-debug/lib -L/media/6c6201d2-4e2e-4b24-8d04-263b5bc06dfa/sanjay/petsc/linux-gnu-c-debug/lib -lscalapack -lsundials_cvode -lsundials_nvecserial -lsundials_nvecparallel -lflapack -lfblas -lX11 -lssl -lcrypto -lpthread -lm -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.6.3 -L/usr/lib/gcc/x86_64-redhat-linux/4.6.3 -lmpichf90 -lgfortran -lm -lgfortran -lm -lquadmath -lm -lmpichcxx -lstdc++ -Wl,-rpath,/media/6c6201d2-4e2e-4b24-8d04-263b5bc06dfa/sanjay/petsc/linux-gnu-c-debug/lib -L/media/6c6201d2-4e2e-4b24-8d04-263b5bc06dfa/sanjay/petsc/linux-gnu-c-debug/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.6.3 -L/usr/lib/gcc/x86_64-redhat-linux/4.6.3 -ldl -Wl,-rpath,/media/6c6201d2-4e2e-4b24-8d04-263b5bc06dfa/sanjay/petsc/linux-gnu-c-debug/lib -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -ldl   -lm -inline-calloc