I can't use candi to compile deal.ii-9.3. Here are the error messages

ASPECT
1

Here are the last few lines from the output of

./candi.sh -p /home/egpuckett/WORKSPACE/deal.ii-9.3.0 -j4

      FC arch-linux2-c-opt/obj/tao/f90-mod/petsctaomod.o
 CLINKER arch-linux2-c-opt/lib/libpetsc.so.3.13.1

Now to install the libraries do:
make PETSC_DIR=/home/egpuckett/WORKSPACE/deal.ii-9.3.0/tmp/build/petsc-lite-3.13.1 PETSC_ARCH=arch-linux2-c-opt install

Fetching slepc 3.13.2
Trying to download https://tjhei.info/candi-mirror/slepc-3.13.2.tar.gz
Total Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 343 100 343 0 0 968 0 --:–:-- --:–:-- --:–:-- 966
100 4689k 100 4689k 0 0 2918k 0 0:00:01 0:00:01 --:–:-- 11.6M
Verifying slepc-3.13.2.tar.gz
slepc-3.13.2.tar.gz: OK(md5)
Unpacking slepc-3.13.2.tar.gz
Building slepc 3.13.2
Checking environment… done
Checking PETSc installation…
ERROR: Unable to link with PETSc
ERROR: See “installed-arch-linux2-c-opt/lib/slepc/conf/configure.log” file for details
Failure with exit status: 1
Exit message: slepc ./configure failed

Here are the contents of

      FC arch-linux2-c-opt/obj/tao/f90-mod/petsctaomod.o
 CLINKER arch-linux2-c-opt/lib/libpetsc.so.3.13.1

Now to install the libraries do:
make PETSC_DIR=/home/egpuckett/WORKSPACE/deal.ii-9.3.0/tmp/build/petsc-lite-3.13.1 PETSC_ARCH=arch-linux2-c-opt install

Fetching slepc 3.13.2
Trying to download https://tjhei.info/candi-mirror/slepc-3.13.2.tar.gz
Total Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 343 100 343 0 0 968 0 --:–:-- --:–:-- --:–:-- 966
100 4689k 100 4689k 0 0 2918k 0 0:00:01 0:00:01 --:–:-- 11.6M
Verifying slepc-3.13.2.tar.gz
slepc-3.13.2.tar.gz: OK(md5)
Unpacking slepc-3.13.2.tar.gz
Building slepc 3.13.2
Checking environment… done
Checking PETSc installation…
ERROR: Unable to link with PETSc
ERROR: See “installed-arch-linux2-c-opt/lib/slepc/conf/configure.log” file for details
Failure with exit status: 1
Exit message: slepc ./configure failed

I’m using standard Ubuntu 20.04 that is updated.

I’ve never had trouble using candi to install deal.ii before. I’ve tried everything I can think of. Thanks

2

Hi Gerry,

Thanks for posting to the forum.

There is no need to install PETSc with candi, as its use in ASPECT is now explicitly disabled.

In the candi.cfg file, you can normally comment out all packages (i.e., this means they won’t be built) except for Trilinos, p4est, and dealii. Other packages you might want to build, depending on what is already installed on your system, are hdf5 and openblas.

Cheers,
John

3

Hi John,

I get an error which says it can build Trilinos when I comment out everything but Trilinos, p4est, and dealii.

I’m starting the error messages at the beginning of the TPL part so you can see what the compiler finds and what it doesn’t:

Processing enabled TPL: MPI (enabled explicitly, disable with -DTPL_ENABLE_MPI=OFF)
Processing enabled TPL: BLAS (enabled by TeuchosNumerics, disable with -DTPL_ENABLE_BLAS=OFF)
– BLAS_LIBRARY_NAMES=‘blas blas_win32’
– Searching for libs in BLAS_LIBRARY_DIRS=’’
– Searching for a lib in the set “blas blas_win32”:
– Searching for lib ‘blas’ …
– Found lib ‘/usr/lib/x86_64-linux-gnu/libblas.so’
– TPL_BLAS_LIBRARIES=’/usr/lib/x86_64-linux-gnu/libblas.so’
Processing enabled TPL: LAPACK (enabled by TeuchosNumerics, disable with -DTPL_ENABLE_LAPACK=OFF)
– LAPACK_LIBRARY_NAMES=‘lapack lapack_win32’
– Searching for libs in LAPACK_LIBRARY_DIRS=’’
– Searching for a lib in the set “lapack lapack_win32”:
– Searching for lib ‘lapack’ …
– Found lib ‘/usr/lib/x86_64-linux-gnu/liblapack.so’
– TPL_LAPACK_LIBRARIES=’/usr/lib/x86_64-linux-gnu/liblapack.so’
Processing enabled TPL: ParMETIS (enabled explicitly, disable with -DTPL_ENABLE_ParMETIS=OFF)
– ParMETIS_LIBRARY_NAMES=‘parmetis;metis’
– TPL_ParMETIS_LIBRARIES=’/home/egpuckett/WORKSPACE/deal.ii-9.3.0/parmetis-4.0.3/lib/libparmetis.so;/home/egpuckett/WORKSPACE/deal.ii-9.3.0/parmetis-4.0.3/lib/libmetis.so’
– TPL_ParMETIS_INCLUDE_DIRS=’/home/egpuckett/WORKSPACE/deal.ii-9.3.0/parmetis-4.0.3/include’
– Performing Test HAVE_PARMETIS_VERSION_4_0_3
– Performing Test HAVE_PARMETIS_VERSION_4_0_3 - Failed
Processing enabled TPL: SCALAPACK (enabled explicitly, disable with -DTPL_ENABLE_SCALAPACK=OFF)
– SCALAPACK_LIBRARY_NAMES=‘scalapack;blacs;blacsF77;blacs’
– Searching for libs in SCALAPACK_LIBRARY_DIRS=’/home/egpuckett/WORKSPACE/deal.ii-9.3.0/petsc-3.13.1/lib’
– Searching for a lib in the set “scalapack”:
– Searching for lib ‘scalapack’ …
– NOTE: Did not find a lib in the lib set “scalapack” for the TPL ‘SCALAPACK’!
– ERROR: Could not find the libraries for the TPL ‘SCALAPACK’!
– TIP: If the TPL ‘SCALAPACK’ is on your system then you can set:
-DSCALAPACK_LIBRARY_DIRS=’;;…’
to point to the directories where these libraries may be found.
Or, just set:
-DTPL_SCALAPACK_LIBRARIES=’;;…’
to point to the full paths for the libraries which will
bypass any search for libraries and these libraries will be used without
question in the build. (But this will result in a build-time error
if not all of the necessary symbols are found.)
– ERROR: Failed finding all of the parts of TPL ‘SCALAPACK’ (see above), Aborting!

– NOTE: The find module file for this failed TPL ‘SCALAPACK’ is:
/home/egpuckett/WORKSPACE/deal.ii-9.3.0/tmp/unpack/Trilinos-trilinos-release-12-18-1/cmake/TPLs/FindTPLSCALAPACK.cmake
which is pointed to in the file:
/home/egpuckett/WORKSPACE/deal.ii-9.3.0/tmp/unpack/Trilinos-trilinos-release-12-18-1/TPLsList.cmake

TIP: Even though the TPL ‘SCALAPACK’ was explicitly enabled in input,
it can be disabled with:
-DTPL_ENABLE_SCALAPACK=OFF
which will disable it and will recursively disable all of the
downstream packages that have required dependencies on it.
When you reconfigure, just grep the cmake stdout for ‘SCALAPACK’
and then follow the disables that occur as a result to see what impact
this TPL disable has on the configuration of Trilinos.

CMake Error at cmake/tribits/core/package_arch/TribitsProcessEnabledTpl.cmake:144 (MESSAGE):
ERROR: TPL_SCALAPACK_NOT_FOUND=TRUE, aborting!
Call Stack (most recent call first):
cmake/tribits/core/package_arch/TribitsGlobalMacros.cmake:1821 (TRIBITS_PROCESS_ENABLED_TPL)
cmake/tribits/core/package_arch/TribitsProjectImpl.cmake:206 (TRIBITS_PROCESS_ENABLED_TPLS)
cmake/tribits/core/package_arch/TribitsProject.cmake:93 (TRIBITS_PROJECT_IMPL)
CMakeLists.txt:90 (TRIBITS_PROJECT)

– Configuring incomplete, errors occurred!
See also “/home/egpuckett/WORKSPACE/deal.ii-9.3.0/tmp/build/trilinos-release-12-18-1/CMakeFiles/CMakeOutput.log”.
See also “/home/egpuckett/WORKSPACE/deal.ii-9.3.0/tmp/build/trilinos-release-12-18-1/CMakeFiles/CMakeError.log”.
Failure with exit status: 1
Exit message: There was a problem configuring trilinos 12-18-1.

Thanks!

  • Gerry
4

Hi Gerry,

It looks like scalapack (and maybe other related libraries) are not installed on the machine.

The instructions in the manual are to install the following packages on Ubuntu:

sudo apt-get install build-essential \
                     cmake \
                     gcc \
                     g++ \
                     gfortran \
                     git \
                     libblas-dev \
                     liblapack-dev \
                     libopenmpi-dev \
                     numdiff \
                     openmpi-bin \
                     zlib1g-dev

Have libblas-dev and liblapack-dev been installed on your computer? These instructions were for Ubuntu 14, so we may need to update to include things like scalapack. See the following link for scalapack libraries to install, depending on the version of MPI on your machine:
https://packages.ubuntu.com/source/bionic/scalapack

I have built deal.II on ubuntu 20.04 with candi, but don’t recall the details of what I installed.

As an alternative, you can have candi install openblas (uncomment that package in candi.cfg) and see if that is sufficient to configure and build Trilinos.

Cheers,
John

5

Hi Gerry,
I might have broken the latest Candi version with a recent change. Can you please do

git remote update
git checkout v9.3.1-r1

and try again?

6

Yup! Starting now … Thanks!

7

Hi Timo,

I still get a failure to build Trilinos … Do you want to see more of the errors. (BTW I’m in a detached HEAD state after git checkout v9.3.1-r1) but I assume that that doesn’t matter

TIP: Even though the TPL ‘SCALAPACK’ was explicitly enabled in input,
it can be disabled with:
-DTPL_ENABLE_SCALAPACK=OFF
which will disable it and will recursively disable all of the
downstream packages that have required dependencies on it.
When you reconfigure, just grep the cmake stdout for ‘SCALAPACK’
and then follow the disables that occur as a result to see what impact
this TPL disable has on the configuration of Trilinos.

CMake Error at cmake/tribits/core/package_arch/TribitsProcessEnabledTpl.cmake:144 (MESSAGE):
ERROR: TPL_SCALAPACK_NOT_FOUND=TRUE, aborting!
Call Stack (most recent call first):
cmake/tribits/core/package_arch/TribitsGlobalMacros.cmake:1821 (TRIBITS_PROCESS_ENABLED_TPL)
cmake/tribits/core/package_arch/TribitsProjectImpl.cmake:206 (TRIBITS_PROCESS_ENABLED_TPLS)
cmake/tribits/core/package_arch/TribitsProject.cmake:93 (TRIBITS_PROJECT_IMPL)
CMakeLists.txt:90 (TRIBITS_PROJECT)

– Configuring incomplete, errors occurred!
See also “/home/egpuckett/WORKSPACE/deal.ii-9.3.0/tmp/build/trilinos-release-12-18-1/CMakeFiles/CMakeOutput.log”.
Failure with exit status: 1
Exit message: There was a problem configuring trilinos 12-18-1.

8

Can you please remove /home/egpuckett/WORKSPACE/deal.ii-9.3.0/tmp/ and try again? This looks like a leftover from earlier.

9

Yup …

10

Nope … How much of the output do you want? Suppose I blow away deal.ii.9.3.0 or even candi and start over?

Short list of error messages

– Configuring incomplete, errors occurred!
See also “/home/egpuckett/WORKSPACE/deal.ii-9.3.0/tmp/build/trilinos-release-12-18-1/CMakeFiles/CMakeOutput.log”.
See also “/home/egpuckett/WORKSPACE/deal.ii-9.3.0/tmp/build/trilinos-release-12-18-1/CMakeFiles/CMakeError.log”.
Failure with exit status: 1
Exit message: There was a problem configuring trilinos 12-18-1.

11

Timo,

What do you think of the following advice? Do you know what the instructions for using “apt …” would be for 20.04. Also shouldn’t we update the manual?

Thanks!

  • G

It looks like scalapack (and maybe other related libraries) are not installed on the machine.

The instructions in the manual are to install the following packages on Ubuntu:

sudo apt-get install build-essential \
                     cmake \
                     gcc \
                     g++ \
                     gfortran \
                     git \
                     libblas-dev \
                     liblapack-dev \
                     libopenmpi-dev \
                     numdiff \
                     openmpi-bin \
                     zlib1g-dev

Have libblas-dev and liblapack-dev been installed on your computer? These instructions were for Ubuntu 14, so we may need to update to include things like scalapack. See the following link for scalapack libraries to install, depending on the version of MPI on your machine:
https://packages.ubuntu.com/source/bionic/scalapack

12

Hi Gerry,

We just switched to requiring 9.3 so the instructions, manual, Candi, etc. likely still need work. I will spend some time on that soon.

Until then, it might be easiest for you to use the Ubuntu packages as you are on 20.04:

Let us know if that works for you.

13

Are you saying ‘don’t use candi’?

14

Correct.

15

Hi all,

Gerry - I just build deal.II 9.3.1 via candi on a desktop with Ubuntu 20.04 freshly installed.

Prior to the installation, I installed all of the recommended ubuntu libraries in the manual and then also installed all of the additional recommended libraries that appear at the beginning of the candi installation process … e.g., I aborted the candi installation, installed additional packages, and then restarted the candi process.

No issues during the installation (HDF5, p4est, Trilinos, deal.II). Can you try installing all of the packages recommended by candi and then trying candi again?

John

16

Hi John,

Could you please send me or post the candi.cfg file that worked here and point me at the part of the manual that lists all of the recommended Ubuntu libraries?

Thanks!

  • Gerry