Can't compile chapter 6 exercise

[ophirnt]

Hello. I am a new reader. I have been trying to do my setup and am testing it by compiling chapter 6's exercise. Unfortunately, it prints out a bunch of errors which doesn't seem related to my petsc installation (which seems to be installed correctly). Sorry for being incovenient, but could someone help me?

~/p4pdes/c/ch6$ make fish
mpicc -o fish.o -c -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -Wno-stringop-overflow -fstack-protector -fvisibility=hidden -g3 -O0 -pedantic -std=c99 -I/opt/ohpc/pub/libs/gnu-13.2.0/openmpi-4.1.5/petsc/3.19.5d/include -I/opt/ohpc/pub/libs/gnu-13.2.0/suitesparse/7.1.0/include -I/opt/ohpc/pub/libs/gnu-13.2.0/openmpi-4.1.5/mumps/5.6.1/include -I/opt/ohpc/pub/libs/gnu-13.2.0/openmpi-4.1.5/trilinos/14.2.0/include -I/opt/ohpc/pub/libs/gnu-13.2.0/openmpi-4.1.5/scotch/7.0.4/include -I/opt/ohpc/pub/libs/gnu-13.2.0/openmpi-4.1.5/netcdf/4.9.2/include -I/opt/ohpc/pub/libs/gnu-13.2.0/openmpi-4.1.5/hdf5/1.14.1d/include -I/opt/ohpc/pub/libs/gnu-13.2.0/openmpi-4.1.5/parmetis/4.0.3/include -I/opt/ohpc/pub/libs/gnu-13.2.0/metis/5.2.1/include -I/opt/ohpc/pub/libs/gnu-13.2.0/libpng/1.6.40/include -I/opt/ohpc/pub/libs/gnu-13.2.0/zlib/1.2.13/include -I/opt/ohpc/pub/libs/gnu-13.2.0/szip/2.1.1/include -I/opt/ohpc/pub/libs/gnu-13.2.0/eigen3/3.4.0/include/eigen3 -I/opt/ohpc/pub/libs/gnu-13.2.0/googletest/1.13.0/include -I/opt/ohpc/pub/libs/gnu-13.2.0/boost/1.82.0/include -I/opt/ohpc/pub/libs/gnu-13.2.0/hwloc/2.9.2/include    `pwd`/fish.c
/home/ophir/p4pdes/c/ch6/fish.c:92:8: error: unknown type name ‘DMDASNESFunctionFn’
   92 | static DMDASNESFunctionFn* residual_ptr[3]
      |        ^~~~~~~~~~~~~~~~~~
/home/ophir/p4pdes/c/ch6/fish.c:93:9: error: ‘DMDASNESFunctionFn’ undeclared here (not in a function); did you mean ‘DMDASNESFunction’?
   93 |     = {(DMDASNESFunctionFn*)&Poisson1DFunctionLocal,
      |         ^~~~~~~~~~~~~~~~~~
      |         DMDASNESFunction
/home/ophir/p4pdes/c/ch6/fish.c:93:28: error: expected expression before ‘)’ token
   93 |     = {(DMDASNESFunctionFn*)&Poisson1DFunctionLocal,
      |                            ^
/home/ophir/p4pdes/c/ch6/fish.c:97:8: error: unknown type name ‘DMDASNESJacobianFn’
   97 | static DMDASNESJacobianFn* jacobian_ptr[3]
      |        ^~~~~~~~~~~~~~~~~~
/home/ophir/p4pdes/c/ch6/fish.c:98:9: error: ‘DMDASNESJacobianFn’ undeclared here (not in a function); did you mean ‘DMDASNESJacobian’?
   98 |     = {(DMDASNESJacobianFn*)&Poisson1DJacobianLocal,
      |         ^~~~~~~~~~~~~~~~~~
      |         DMDASNESJacobian
/home/ophir/p4pdes/c/ch6/fish.c:98:28: error: expected expression before ‘)’ token
   98 |     = {(DMDASNESJacobianFn*)&Poisson1DJacobianLocal,
      |                            ^
In file included from /opt/ohpc/pub/libs/gnu-13.2.0/openmpi-4.1.5/petsc/3.19.5d/include/petscsys.h:1086,
                 from /opt/ohpc/pub/libs/gnu-13.2.0/openmpi-4.1.5/petsc/3.19.5d/include/petscbag.h:5,
                 from /opt/ohpc/pub/libs/gnu-13.2.0/openmpi-4.1.5/petsc/3.19.5d/include/petsc.h:5,
                 from /home/ophir/p4pdes/c/ch6/fish.c:10:
/home/ophir/p4pdes/c/ch6/fish.c: In function ‘main’:
/home/ophir/p4pdes/c/ch6/fish.c:226:35: error: expected expression before ‘)’ token
  226 |              (DMDASNESFunctionFn *)(residual_ptr[dim-1]),&user));
      |                                   ^
/opt/ohpc/pub/libs/gnu-13.2.0/openmpi-4.1.5/petsc/3.19.5d/include/petscerror.h:461:28: note: in definition of macro ‘PetscCall’
  461 |       ierr_petsc_call_q_ = __VA_ARGS__; \
      |                            ^~~~~~~~~~~
/home/ophir/p4pdes/c/ch6/fish.c:228:35: error: expected expression before ‘)’ token
  228 |              (DMDASNESJacobianFn *)(jacobian_ptr[dim-1]),&user));
      |                                   ^
/opt/ohpc/pub/libs/gnu-13.2.0/openmpi-4.1.5/petsc/3.19.5d/include/petscerror.h:461:28: note: in definition of macro ‘PetscCall’
  461 |       ierr_petsc_call_q_ = __VA_ARGS__; \
      |                            ^~~~~~~~~~~
make: *** [/opt/ohpc/pub/libs/gnu-13.2.0/openmpi-4.1.5/petsc/3.19.5d/lib/petsc/conf/rules:148: fish.o] Error 1

[bueler]

It looks like your PETSc version is not the most recent. Please do something like
$ ls $PETSC_DIR/$PETSC_ARCH/lib/ |grep libpetsc
to get your installed petsc version number.

Then go to the p4pdes releases list and get/checkout the right tag, or download the version which matches your petsc version number.

If this does not work please let me know and we will try again?

[ophirnt]

Guess that must be it then. I just simply cloned the repo and tried compiling. The apt version must be out of date, as usual. I'll try downloading for version 3.19 or simply compiling the newer PETSc version later and will send news. Thank you very much!

ls $PETSC_DIR/lib/ | grep libpetsc
libpetsc.so
libpetsc.so.3.19
libpetsc.so.3.19.5

[bueler]

Got it. Your debian system has petsc 3.19.5 which is a year old (?). You can build petsc from source if you want to use the most recent p4pdes download. Alternatively, you can grab this p4pdes release and it should work:
https://github.com/bueler/p4pdes/releases/tag/v3.20.0

[ophirnt]

Yes, I just built the new release (very easy actually). Working like a charm now, thank you very much!

I could add a pull request with this caveat added for future users not get confused. What do you think?

[bueler]

I could add a pull request with this caveat added for future users not get confused. What do you think?

I definitely welcome pull requests but I am not quite sure what you have in mind. Thanks, Ed

[ophirnt]

I've just added this bullet point:

  * My book does not contain PETSc installation instructions, though it has
    minimal advice.  Maintaining installation information is the job of
    PETSc developers, not me.  (Thank goodness.)
  * [CONFIGS.md](CONFIGS.md) contains some of the `configure` commands which
    work on the author's machines.  These are minimal installation suggestions.
  * My book does not help the reader with debugging C programs.k does not help the reader with debugging C programs.
  --> * Make sure to [download a release](https://github.com/bueler/p4pdes/releases/) compatible with your computer's PETSc version. Package managers (such as apt) may only contain older versions of PETSc that are incompatible with newer releases of p4pdes.

I can't upload the changes to a branch and do the pull request, though.

[bueler]

Ophir -- Thanks for this suggestion! I went ahead and made the change. Ed

…

On Thu, May 2, 2024 at 8:00 PM Ophir ***@***.***> wrote: I've just added this bullet point: * My book does not contain PETSc installation instructions, though it has minimal advice. Maintaining installation information is the job of PETSc developers, not me. (Thank goodness.) * [CONFIGS.md](CONFIGS.md) contains some of the `configure` commands which work on the author's machines. These are minimal installation suggestions. * My book does not help the reader with debugging C programs.k does not help the reader with debugging C programs. --> * Make sure to [download a release](https://github.com/bueler/p4pdes/releases/) compatible with your computer's PETSc version. Package managers (such as apt) may only contain older versions of PETSc that are incompatible with newer releases of p4pdes. I can't upload the changes to a branch and do the pull request, though. — Reply to this email directly, view it on GitHub <#57 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAINQT5UA2WU7NYK6TYUDSDZAMDU3AVCNFSM6AAAAABHAW3TECVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJSGA3TQNBXHE> . You are receiving this because you commented.Message ID: ***@***.***>

-- Ed Bueler Dept of Mathematics and Statistics, University of Alaska Fairbanks Fairbanks, AK 99775-6660 office: 306C Chapman website: https://bueler.github.io/