Thread: Need a jumpstart compiling using GCC in BASH/Linux

Hi. I have some programming background coding for applications (think things like coding for Excel, MS Word, etc.). But I'm back in school and for my math thesis I need to compile a C program using gcc, using SUNDIALS (an ODE solver) library, on Linux. I had a little experience with C over 20 years ago; I've never used Linux, BASH, gcc, or SUNDIALS.

I think I've installed SUNDIALS correctly, but to test that out, I need to compile one of their example programs. To compile, I need to learn Linux/BASH, gcc, and C. I just don't have the time to do all that reading and I would like it if someone could quickly show me how to compile the attached code (and give a few clues on what to look for to compile my own code, too).

I apologize for posting a question without doing all the requisite reading and promise to make future questions more germane.

cvAdvDiff_non_p..c

Thanks, in advance.

You don't really need to learn bash just for compiling:
Just write "gcc filename.c -o output" and you're done. (You may need to pass gcc a few other options)

Originally Posted by manasij7479

You don't really need to learn bash just for compiling:
Just write "gcc filename.c -o output" and you're done. (You may need to pass gcc a few other options)

I should have mentioned that I already tried that. Here is the output I got (I can't get this to display correctly, so attaching it, too): cvode.out.txt

Code:

$ gcc cvAdvDiff_non_p.c -o 
cvAdvDiff_non_p.outcvAdvDiff_non_p.c:37:71: error: cvode/cvode.h: No such file or directory

cvAdvDiff_non_p.c:38:78: error: nvector/nvector_parallel.h: No such file or directory

cvAdvDiff_non_p.c:39:67: error: sundials/sundials_types.h: No such file or directory

cvAdvDiff_non_p.c:40:62: error: sundials/sundials_math.h: No such file or directory

cvAdvDiff_non_p.c:42:68: error: mpi.h: No such file or directory

cvAdvDiff_non_p.c:61: error: expected specifier-qualifier-list before 'realtype'

cvAdvDiff_non_p.c:69: error: expected ')' before 'u'

cvAdvDiff_non_p.c:74: error: expected ')' before 't'

cvAdvDiff_non_p.c:80: error: expected ')' before 't'

cvAdvDiff_non_p.c: In function 'main':

cvAdvDiff_non_p.c:90: error: 'realtype' undeclared (first use in this function)

cvAdvDiff_non_p.c:90: error: (Each undeclared identifier is reported only once

cvAdvDiff_non_p.c:90: error: for each function it appears in.)

cvAdvDiff_non_p.c:90: error: expected ';' before 'dx'

cvAdvDiff_non_p.c:91: error: 'N_Vector' undeclared (first use in this function)

cvAdvDiff_non_p.c:91: error: expected ';' before 'u'

cvAdvDiff_non_p.c:97: error: 'MPI_Comm' undeclared (first use in this function)

cvAdvDiff_non_p.c:97: error: expected ';' before 'comm'

cvAdvDiff_non_p.c:99: error: 'u' undeclared (first use in this function)

cvAdvDiff_non_p.c:105: error: 'comm' undeclared (first use in this function)

cvAdvDiff_non_p.c:105: error: 'MPI_COMM_WORLD' undeclared (first use in this function)

cvAdvDiff_non_p.c:118: error: 'struct <anonymous>' has no member named 'comm'

cvAdvDiff_non_p.c:119: error: 'struct <anonymous>' has no member named 'npes'

cvAdvDiff_non_p.c:120: error: 'struct <anonymous>' has no member named 'my_pe'

cvAdvDiff_non_p.c:125: error: 'reltol' undeclared (first use in this function)

cvAdvDiff_non_p.c:126: error: 'abstol' undeclared (first use in this function)

cvAdvDiff_non_p.c:128: error: 'dx' undeclared (first use in this function)

cvAdvDiff_non_p.c:128: error: 'struct <anonymous>' has no member named 'dx'

cvAdvDiff_non_p.c:129: error: 'struct <anonymous>' has no member named 'hdcoef'

cvAdvDiff_non_p.c:130: error: 'struct <anonymous>' has no member named 'hacoef'

cvAdvDiff_non_p.c:136: error: 'CV_ADAMS' undeclared (first use in this function)

cvAdvDiff_non_p.c:136: error: 'CV_FUNCTIONAL' undeclared (first use in this function)

cvAdvDiff_non_p.c:145: error: 'f' undeclared (first use in this function)

cvAdvDiff_non_p.c:155: error: 'umax' undeclared (first use in this function)

cvAdvDiff_non_p.c:158: error: 't' undeclared (first use in this function)

cvAdvDiff_non_p.c:164: error: 'tout' undeclared (first use in this function)

cvAdvDiff_non_p.c:165: error: 'CV_NORMAL' undeclared (first use in this function)

cvAdvDiff_non_p.c: At top level:

cvAdvDiff_non_p.c:189: error: expected ')' before 'u'

cvAdvDiff_non_p.c:221: error: expected ')' before 't'

cvAdvDiff_non_p.c:262: error: expected ')' before 't'

Originally Posted by Salem

Lets say you download a library and you put it in say /home/user/mylibs/magic
Within this directory are further directories called include and lib.
These respectively contain magic.h and libmagic.a

Your source code begins with

Code:

#include <magic.h>

and goes onto use various functions.

The way you compile is by saying
gcc -I/home/user/mylibs/magic/include -L/home/user/mylibs/magic/lib prog.c -lmagic

OK. I have to go figure out where the correct include and lib directories are. I'll report back. Thanks.

Originally Posted by CCompiler

OK. I have to go figure out where the correct include and lib directories are. I'll report back. Thanks.

Right inside your downloaded folder.

Originally Posted by manasij7479

Right inside your downloaded folder.

This was not a routine install. I have an include directory, but it has no files in it . There is no directory called lib​, so I had to look for the library directory, too.

Anyway, I came up with this:

Code:

gcc -I/home/<username>/sundials/cvode-2.6.0/include -L/home/<username>/sundials/cvode-2.6.0/instdir/lib cvAdvDiff_non_p.c

I saved that line to a file called cvAdvDiff_non_p.make. I typed

Code:

$ chmod +x cvAdvDiff_non_p.make

to make it executable. Then typed

Code:

./cvAdvDiff_non_p.make >cvAdvDiff_non_p.out

.

There is nothing in the file cvAdvDiff_non_p.out, but the screen showed a whole bunch of errors, which I can't upload. It starts like this:

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:
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:73: error: expected specifier-qualifier-list before 'realtype'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:316: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'N_Vector'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:317: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'N_Vector'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:318: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'void'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:319: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'void'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:320: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'realtype'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:321: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'void'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:322: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'void'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:323: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'void'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:324: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'void'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:325: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'void'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:326: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'void'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:327: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'void'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:328: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'void'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:329: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'void'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:330: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'realtype'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:331: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'realtype'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:332: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'realtype'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:333: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'realtype'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:334: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'realtype'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:335: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'realtype'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:336: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'realtype'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:337: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'void'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:338: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'int'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:339: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'int'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:340: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'realtype'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:365: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'N_Vector'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:366: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'N_Vector'
/home/schwarz/sundials/cvode-2.6.0/include/sundials/sundials_nvector.h:367: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'void'
In file included from cvAdvDiff_non_p.c:37:
/home/schwarz/sundials/cvode-2.6.0/include/cvode/cvode.h:155: error: expected ')' before 't'
/home/schwarz/sundials/cvode-2.6.0/include/cvode/cvode.h:177: error: expected ')' before 't'
/home/schwarz/sundials/cvode-2.6.0/include/cvode/cvode.h:253: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'void'
/home/schwarz/sundials/cvode-2.6.0/include/cvode/cvode.h:365: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'int'
/home/schwarz/sundials/cvode-2.6.0/include/cvode/cvode.h:366: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'int'
/home/schwarz/sundials/cvode-2.6.0/include/cvode/cvode.h:367: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'int'
/home/schwarz/sundials/cvode-2.6.0/include/cvode/cvode.h:368: error: expected '=', ',', ';

Anybody know what this says is wrong? Or how I can fix it? (Sorry for being so obtuse - and thanks for your help).

Originally Posted by Salem

OK, so do you know where make install copied the files?

/usr/include and /usr/lib would seem like good places to look.

The documentation should tell you where.

I had to do the install in my own account, so all the files are in '/home/<myusername>'.

There is an include directory, '/home/<username>/sundials/cvode-2.6.0/include', but it has only subdirectories in it (called cvode, nvector, sundials).

There is no lib directory, but there is one called src, '/home/<username>/sundials/cvode-2.6.0/src'

The full directory list under cvode-2.6.0 are:
bin
builddir
config
doc
examples
include
instdir
src

Are include and src the directories I'm looking for?

Originally Posted by Salem

What about in instdir?

You could try
find . -name "*.a"
from the project root, to see if any .a files have been created.

Salem, thanks for helping out.

I'm using '/home/<username>/sundials/cvode-2.6.0' as the project root. Here's what I get

$ find . -name "*.a"
./builddir/src/nvec_par/.libs/libsundials_nvecparallel.a
./builddir/src/nvec_ser/.libs/libsundials_nvecserial.a
./builddir/src/cvode/.libs/libsundials_cvode.a
./instdir/lib/libsundials_nvecserial.a
./instdir/lib/libsundials_cvode.a
./instdir/lib/libsundials_nvecparallel.a

I recall creating the name instdir during one attempt at installation. I guess './instdir/lib' is the lib directory.

I created cvAdvDiff_non_p.make using those directories, like this:

projDir='/home/<username>/sundials/cvode-2.6.0'
gcc -I$projDir$/instdir/include -L$projDir$/instdir/lib/ cvAdvDiff_non_p.c

Then I tried compiling and got the same errors.

$ ./cvAdvDiff_non_p.make
cvAdvDiff_non_p.c:37:71: error: cvode/cvode.h: No such file or directory
cvAdvDiff_non_p.c:38:78: error: nvector/nvector_parallel.h: No such file or directory
cvAdvDiff_non_p.c:39:67: error: sundials/sundials_types.h: No such file or directory
cvAdvDiff_non_p.c:40:62: error: sundials/sundials_math.h: No such file or directory
cvAdvDiff_non_p.c:42:68: error: mpi.h: No such file or directory
cvAdvDiff_non_p.c:61: error: expected specifier-qualifier-list before 'realtype'
cvAdvDiff_non_p.c:69: error: expected ')' before 'u'
cvAdvDiff_non_p.c:74: error: expected ')' before 't'
cvAdvDiff_non_p.c:80: error: expected ')' before 't'
cvAdvDiff_non_p.c: In function 'main':
cvAdvDiff_non_p.c:90: error: 'realtype' undeclared (first use in this function)
cvAdvDiff_non_p.c:90: error: (Each undeclared identifier is reported only once
cvAdvDiff_non_p.c:90: error: for each function it appears in.)
cvAdvDiff_non_p.c:90: error: expected ';' before 'dx'
cvAdvDiff_non_p.c:91: error: 'N_Vector' undeclared (first use in this function)
cvAdvDiff_non_p.c:91: error: expected ';' before 'u'
cvAdvDiff_non_p.c:97: error: 'MPI_Comm' undeclared (first use in this function)
cvAdvDiff_non_p.c:97: error: expected ';' before 'comm'
cvAdvDiff_non_p.c:99: error: 'u' undeclared (first use in this function)
cvAdvDiff_non_p.c:105: error: 'comm' undeclared (first use in this function)
cvAdvDiff_non_p.c:105: error: 'MPI_COMM_WORLD' undeclared (first use in this function)
cvAdvDiff_non_p.c:118: error: 'struct <anonymous>' has no member named 'comm'
cvAdvDiff_non_p.c:119: error: 'struct <anonymous>' has no member named 'npes'
cvAdvDiff_non_p.c:120: error: 'struct <anonymous>' has no member named 'my_pe'
cvAdvDiff_non_p.c:125: error: 'reltol' undeclared (first use in this function)
cvAdvDiff_non_p.c:126: error: 'abstol' undeclared (first use in this function)
cvAdvDiff_non_p.c:128: error: 'dx' undeclared (first use in this function)
cvAdvDiff_non_p.c:128: error: 'struct <anonymous>' has no member named 'dx'
cvAdvDiff_non_p.c:129: error: 'struct <anonymous>' has no member named 'hdcoef'
cvAdvDiff_non_p.c:130: error: 'struct <anonymous>' has no member named 'hacoef'
cvAdvDiff_non_p.c:136: error: 'CV_ADAMS' undeclared (first use in this function)
cvAdvDiff_non_p.c:136: error: 'CV_FUNCTIONAL' undeclared (first use in this function)
cvAdvDiff_non_p.c:145: error: 'f' undeclared (first use in this function)
cvAdvDiff_non_p.c:155: error: 'umax' undeclared (first use in this function)
cvAdvDiff_non_p.c:158: error: 't' undeclared (first use in this function)
cvAdvDiff_non_p.c:164: error: 'tout' undeclared (first use in this function)
cvAdvDiff_non_p.c:165: error: 'CV_NORMAL' undeclared (first use in this function)
cvAdvDiff_non_p.c: At top level:
cvAdvDiff_non_p.c:189: error: expected ')' before 'u'
cvAdvDiff_non_p.c:221: error: expected ')' before 't'
cvAdvDiff_non_p.c:262: error: expected ')' before 't'

Is there something wrong with cvAdvDiff_non_p.make, or do I still have the directories wrong (or both)?