Thread: Library's library can't be found (Stupid newbie needs help compiling)

This is a followup to this. I made a little bit of progress, but I'm still flummoxed. I have a more specific question this time.

I am trying to compile a sample program which came with a software package I installed called SUNDIALS. The code is correct (it is supplied as an example with the code).

However, I am getting an error message which indicates that a library cannot find one of the libraries referenced in its #include statement. But the file that it cannot find is in the same directory.

So I am compiling the file /home/<myusername>/sundials/srcdir/examples/cvode/parallelcvAdvDiff_non_p.c, which starts like this:

Code:

#include <stdio.h>#include <stdlib.h>
#include <math.h>


#include <cvode/cvode.h>              /* prototypes for CVODE fcts. */
#include <nvector/nvector_parallel.h> /* definition of N_Vector and macros */
#include <sundials/sundials_types.h>  /* definition of realtype */
#include <sundials/sundials_math.h>   /* definition of EXP */


#include <mpi.h>                      /* MPI constants and types */
...

See the #include <sundials/sundials_types.h>? That file's full location is /home/<myusername>/sundials/srcdir/include/sundials/sundials_types. The compiler finds it. It starts

Code:

#ifndef _SUNDIALSTYPES_H#define _SUNDIALSTYPES_H


#ifdef __cplusplus  /* wrapper to enable C++ usage */
extern "C" {
#endif


#ifndef _SUNDIALS_CONFIG_H
#define _SUNDIALS_CONFIG_H
#include <sundials/sundials_config.h>
#endif


#include <float.h>

Now, see the line #include <sundials/sundials_config.h>? That file is in the same directory as sundials_types., but the compiler can't find it.

The compile command I'm using is

Code:

$ gcc -I/home/schwarz/sundials/cvode-2.6.0/include -L/home/schwarz/sundials/cvode-2.6.0/instdir/lib/ cvAdvDiff_non_p.c

The start of the error message I'm getting is

Code:

In file included from /home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:50,
                 from /home/schwarz/sundials/cvode-2.6.0/include/cvode/cvode.h:37,
                 from cvAdvDiff_non_p.c:37:
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_types.h:50:38: error: sundials/sundials_config.h: No such file or directory
In file included from /home/schwarz/sundials/cvode-2.6.0/include/cvode/cvode.h:37,
                 from cvAdvDiff_non_p.c:37:

Anybody know why the compiler doesn't find the library's library? How do I fix that?

Originally Posted by Salem

You've specified where to look, but you didn't specify what to look for.

Look at the end of the command line in the previous post.
You also need the name(s) of the libraries you want to link with.

Hi Salem. I'm not following you. What is the option which tells what to look for (I paged through the 12000 pages of man gcc), and what are the choices. Thanks.

Did you run ./configure? I think you're trying to compile a file which has not been pre-processed. You shouldn't be using files in the src/ directory, but in the install-root/examples directory.

Code:

neon:sundials-2.4.0 rags$ ./configure --prefix=`pwd`/ctest
---------------------------------
Running SUNDIALS Configure Script
---------------------------------

Initialization
--------------

checking build system type... i386-apple-darwin10.8.0
checking host system type... i386-apple-darwin10.8.0
checking whether make sets $(MAKE)... yes
checking for a BSD-compatible install... /opt/local/bin/ginstall -c
<snip>

  Type 'make' and then 'make install' to build and install SUNDIALS 2.4.0.

----------------------------------
Finished SUNDIALS Configure Script
----------------------------------

neon:sundials-2.4.0 rags$ make
----------------------
Make src/sundials...
----------------------
<snip>

neon:sundials-2.4.0 rags$ make install
/bin/sh ./config/mkinstalldirs /Users/rags/Downloads/sundials-2.4.0/ctest/bin
mkdir -p -- /Users/rags/Downloads/sundials-2.4.0/ctest/bin
/opt/local/bin/ginstall -c  ./bin/sundials-config    /Users/rags/Downloads/sundials-2.4.0/ctest/bin/
----------------------
Install src/sundials...
----------------------
<snip>

neon:sundials-2.4.0 rags$ cd ctest/
neon:ctest rags$ ls
bin/		include/	lib/
neon:ctest rags$ cd lib/
neon:lib rags$ ls
libsundials_cvode.a		libsundials_idas.la*
libsundials_cvode.la*		libsundials_kinsol.a
libsundials_cvodes.a		libsundials_kinsol.la*
libsundials_cvodes.la*		libsundials_nvecparallel.a
libsundials_ida.a		libsundials_nvecparallel.la*
libsundials_ida.la*		libsundials_nvecserial.a
libsundials_idas.a		libsundials_nvecserial.la*


neon:sundials-2.4.0 rags$ gcc -Ictest/include -Lctest/lib examples/cvode/parallel/cvAdvDiff_non_p.c -o mytest -lsundials_cvode -lmpi -lsundials_nvecparallel 
neon:sundials-2.4.0 rags$ ls
CMakeLists.txt	README		config.h	configure.ac	libtool*
INSTALL_NOTES	a.out*		config.hin	ctest/		mytest*
LICENSE		acinclude.m4	config.log	doc/		src/
Makefile	bin/		config.status*	examples/	sundialsTB/
Makefile.in	config/		configure*	include/
neon:sundials-2.4.0 rags$ ./mytest 

 1-D advection-diffusion equation, mesh size = 10 

 Number of PEs =   1 

At t = 0.00  max.norm(u) =  1.569909e+01  nst =   0 
At t = 0.50  max.norm(u) =  3.052881e+00  nst = 113 
At t = 1.00  max.norm(u) =  8.753188e-01  nst = 191 
At t = 1.50  max.norm(u) =  2.494926e-01  nst = 265 
At t = 2.00  max.norm(u) =  7.109437e-02  nst = 332 
At t = 2.50  max.norm(u) =  2.026175e-02  nst = 405 
At t = 3.00  max.norm(u) =  5.776619e-03  nst = 473 
At t = 3.50  max.norm(u) =  1.653843e-03  nst = 540 
At t = 4.00  max.norm(u) =  4.740297e-04  nst = 626 
At t = 4.50  max.norm(u) =  1.361421e-04  nst = 694 
At t = 5.00  max.norm(u) =  3.864269e-05  nst = 766 

Final Statistics: 

nst = 766     nfe  = 1437    nni = 1433    ncfn = 139     netf = 5

I did run ./configure. This is how I installed the program:

Code:

$ cd cvode-2.6.0
$ mkdir builddir
$ ./configure --prefix=/home/schwarz/sundials/srcdir/instdir --enable-examples --with-precision=extended --enable-shared
$ make
$ make install

Well I downloaded the sundials package, and documented pretty much everything from configure to compiling an example above. Don't know what else to tell you.

OK, I downloaded the package you did, configured and installed it as you did, then did this:
Compiled and linked, creating an executable named cvAdvDiff_non_p from the file cvAdvDiff_non_p.c:

Code:

neon:cvode-2.6.0 rags$ gcc -I$HOME/sundials/srcdir/instdir/include -L$HOME/sundials/srcdir/instdir/lib $HOME/sundials/srcdir/instdir/examples/cvode/parallel/cvAdvDiff_non_p.c -o cvAdvDiff_non-p -lsundials_cvode -lmpi -lsundials_nvecparallel

Then ran it:

Code:

neon:cvode-2.6.0 rags$ ./cvAdvDiff_non-p  1-D advection-diffusion equation, mesh size = 10 

 Number of PEs =   1 

At t = 0.00  max.norm(u) =  1.569909e+01  nst =   0 
At t = 0.50  max.norm(u) =  3.052881e+00  nst = 113 
At t = 1.00  max.norm(u) =  8.753188e-01  nst = 191 
At t = 1.50  max.norm(u) =  2.494926e-01  nst = 265 
At t = 2.00  max.norm(u) =  7.109437e-02  nst = 332 
At t = 2.50  max.norm(u) =  2.026175e-02  nst = 405 
At t = 3.00  max.norm(u) =  5.776619e-03  nst = 473 
At t = 3.50  max.norm(u) =  1.653843e-03  nst = 540 
At t = 4.00  max.norm(u) =  4.740297e-04  nst = 626 
At t = 4.50  max.norm(u) =  1.361421e-04  nst = 694 
At t = 5.00  max.norm(u) =  3.864269e-05  nst = 766 

Final Statistics: 

nst = 766     nfe  = 1437    nni = 1433    ncfn = 139     netf = 5

OK? Help you?

Hey all. I lucked out when a friend of a friend who has good Linux experience agreed to help me. It's a good thing, too, because I was waaay off. You all couldn't help me because I didn't understand enough and wasn't giving you nearly enough information.

The end result is that we got it working. For those curious about the answer, we had to update an environment variable (which I conveniently forgot to write down!) and ended up with the following "make" file which hardly looked like it came from the one earlier in this thread:

Code:

projDir='/home/schwarz/sundials/srcdir/'
mpicc -I${projDir}instdir/include -I/usr/local/mpi/include -L${projDir}instdir/lib -L/usr/local/mpi/lib cvAdvDiff_non_p.c -lpthread -lsundials_cvode -lsundials_nvecparallel -o cvAdvDiff_non_p.out -Wl,-R,/home/schwarz/sundials/srcdir/instdir/lib

I don't understand all of this yet, but fortunately my friend's friend is a coffee nut and he's in my area often. He agreed to teach me a little in return for some Starbucks on Friday.

Thanks all for your help. Feel free to post any hints you can glean from the final answer which might help me.