Building NGSolve from scratch trouble

Installation & Troubleshooting
1

I am trying to build NGSolve from source. When I get to the part where I call cmake:

cmake -DUSE_MPI=ON -DUSE_MKL=ON -DUSE_OCC=ON -DUSE_MPI=ON -DUSE_MUMPS=ON -DUSE_PARDISO=ON -DUSE_UMFPACK=ON -DMKL_ROOT=/usr/share/intel-mkl -DCMAKE_INSTALL_PREFIX={BASEDIR}/ngsolve-install {BASEDIR}/ngsolve-src

this happens:

– Configuring incomplete, errors occurred!
See also “/home/walker/ngsuite/ngsolve-build/netgen/CMakeFiles/CMakeOutput.log”.
CMake Warning (dev) at cmake/SuperBuild.cmake:175 (find_package):
Policy CMP0074 is not set: find_package uses _ROOT variables.
Run “cmake --help-policy CMP0074” for policy details. Use the cmake_policy
command to set the policy and suppress this warning.

CMake variable MKL_ROOT is set to:

/usr/share/intel-mkl

For compatibility, CMake is ignoring the variable.
Call Stack (most recent call first):
CMakeLists.txt:56 (include)
This warning is for project developers. Use -Wno-dev to suppress it.

– Could NOT find MKL (missing: MKL_DIR)
CMake Error at /usr/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
Could NOT find MKL (missing: MKL_INCLUDE_DIR)
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE)
cmake/cmake_modules/FindMKL.cmake:151 (find_package_handle_standard_args)
cmake/SuperBuild.cmake:175 (find_package)
CMakeLists.txt:56 (include)

I’m pretty sure that is the correct directory for MKL. However, it seems that cmake is just ignoring it. What should I do?

2

Hi,

there some changes to how NGSolve tries to find MKL, so that now it uses the oneAPI MKLConfig.cmake script to locate MKL. Maybe give it a try without specifying MKL_ROOT? Before this change to ngsolve, I used the flag -DMKL_LIBRARY=${MKL_ROOT}/lib/libmkl_rt.so.2 which helped to locate MKL.

Best wishes,
Henry

3

Ok, so I should install the oneAPI MKL stuff. I didn’t do that.

4

The actual flag I had to pass to cmake is:

-DMKL_INCLUDE_DIR=/usr/include/mkl

In other words, MKL_ROOT is not used anymore (NGSolve webpage about cmake flags is out of date).

5

Another issue:

So I proceed with “make”, and it hangs when trying to download mumps. Apparently, the URL for downloading it: http://mumps.enseeiht.fr/MUMPS_5.2.0.tar.gz

is no longer active. Also, it seems one is really supposed to get MUMPS through the official website. I’m trying to do that now. But what version is supported by NGSolve?

6

Alright, I made a little more progress. I was able to get the MUMPS tar ball, with the correct checksum.

However, when I proceed with “make”, it fails:

walker@LAPTOP-NGO6EPCF:~/ngsuite/ngsolve-build$ make
[ 0%] Built target check_submodules_start
[ 19%] Built target project_parmetis
[ 21%] Performing download step (download, verify and extract) for ‘project_mumps’
– verifying file…
file=‘/home/walker/ngsuite/ngsolve-src/external_dependencies/MUMPS_5.2.0.tar.gz’
– File already exists and hash match (skip download):
file=‘/home/walker/ngsuite/ngsolve-src/external_dependencies/MUMPS_5.2.0.tar.gz’
MD5=‘cd6d06f27ce2689eb0436e41fcc9caed’
– extracting…
src=‘/home/walker/ngsuite/ngsolve-src/external_dependencies/MUMPS_5.2.0.tar.gz’
dst=‘/home/walker/ngsuite/ngsolve-build/dependencies/src/project_mumps’
– extracting… [tar xfz]
– extracting… [analysis]
– extracting… [rename]
– extracting… [clean up]
– extracting… done
[ 23%] Performing update step for ‘project_mumps’
[ 26%] No patch step for ‘project_mumps’
[ 28%] No configure step for ‘project_mumps’
[ 30%] Performing build step for ‘project_mumps’
ana_orderings_wrappers_m.F:315:39:

314 | CALL MUMPS_COPY_INT_32TO64 (FRERE(1), NCMP, FRERE8)
| 2
315 | CALL MUMPS_COPY_INT_32TO64 (OPTIONS_METIS, LOPTIONS_METIS,
| 1
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (scalar and rank-1)
ana_orderings_wrappers_m.F:318:29: …

I stopped the output. Similar errors are reported.

I guess I have the wrong compiler configured?? Any suggestions?

-Shawn

7

Ok, I was able to adjust the compiler flags, and it get past that previous post.

However, it seems to get hung up on MUMPS:

(NGS) walker@LAPTOP-NGO6EPCF:~/ngsuite/ngsolve-build$ make -j4
[ 38%] Built target project_parmetis
[ 38%] Built target suitesparse
[ 40%] Performing update step for ‘project_mumps’
[ 42%] Performing build step for ‘netgen_project’
make[3]: *** No targets specified and no makefile found. Stop.
make[2]: *** [CMakeFiles/netgen_project.dir/build.make:86: dependencies/src/netgen_project-stamp/netgen_project-build] Error 2
make[1]: *** [CMakeFiles/Makefile2:150: CMakeFiles/netgen_project.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs…
[ 45%] No patch step for ‘project_mumps’
[ 47%] No configure step for ‘project_mumps’
[ 47%] Built target check_submodules_start
[ 50%] Performing build step for ‘project_mumps’
make[3]: warning: -j1 forced in submake: resetting jobserver mode.
[ 52%] No install step for ‘project_mumps’
[ 54%] Completed ‘project_mumps’
[ 59%] Built target project_mumps
make: *** [Makefile:156: all] Error 2

What is the issue? It found MUMPS previously and was able to compile.

8

Also, I noticed in-between yesterday and today, the install script changed the MUMPS version from 5.2.0 to 5.0.2. Was this a mistake?

9

Hi Shawn,

I was about to fix your issues, yes the other Version was a mistake.

Also there was an issue with finding MKL Scalapack (a fix is in the pipeline and will be uploaded soon).

Best,
Matthias

Edit: The code is now up to date.

10

Ok, thanks. But in the meantime, I turned off MUMPS. I then ran into an issue with Pardiso. When I run cmake, I get this:

– Could NOT find MKL (missing: MKL_DIR)

Even if I include a flag: -DMKL_DIR=/the_path/

I still get that error. If I proceed with “make”, it goes through most stuff, except Pardiso.

11

Do I need to set a cmake policy? There is something about this:

Policy CMP0074 is not set: find_package uses _ROOT variables.
Run “cmake --help-policy CMP0074” for policy details. Use the cmake_policy
command to set the policy and suppress this warning.

It seems that MKL_ROOT is ignored because of this policy. Do I need to change it? If so, then I have to modify the cmake files.

12

I always set MKLROOT and MKL_ROOT and I vaguely remember there is a reason for it… I think the find package needs both set

13

Are you kidding me? That is ridiculous.

14

Ok, I’m making slow progress. It seems that MKLROOT should be an environment variable. So I did that. However, when I run the following cmake command:

cmake -DUSE_MPI=ON -DUSE_MKL=ON -DMKL_INCLUDE_DIR=/opt/intel/oneapi/mkl/2023.2.0/include -DMKL_ROOT=/opt/intel/oneapi -DUSE_MUMPS=ON -DCMAKE_INSTALL_PREFIX={BASEDIR}/ngsolve-install {BASEDIR}/ngsolve-src

I get this:

…stuff…
– Found MKL: intelmpi
CMake Error at /usr/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
Could NOT find MKL (missing: MKL_INCLUDE)
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE)
/usr/local/lib/cmake/mkl-2023.2.0/MKLConfig.cmake:438 (find_package_handle_standard_args)
cmake/cmake_modules/FindMKL.cmake:36 (find_package)
cmake/SuperBuild.cmake:175 (find_package)
CMakeLists.txt:58 (include)

– Configuring incomplete, errors occurred!
See also “/home/walker/ngsuite/ngsolve-build/CMakeFiles/CMakeOutput.log”.

It says it is missing MKL_INCLUDE. I have not gotten this before; I got a missing a MKL_INCLUDE_DIR before, but not this.

Any suggestions?

-Shawn

15

I’m having better luck now…

16

Ok, I succeeded in compiling from source. With MPI and MKL. netgen works and I can run a navier-stokes example. However, I have an issue with jupyter notebook. I’ll post another thread.

17

Ok, I went back and tried to add OpenCascade to my cmake command with:
-DUSE_OCC=ON

After cmake, I run make, and I eventually get this:
No rule to make target ‘/usr/lib/x86_64-linux-gnu/libtbb.so’, needed by ‘libnglib.so’. Stop.

What exactly is the problem? Do I need to install something else beforehand? Note: I also added these flags to my cmake:
-DUSE_PARDISO=ON -DUSE_UMFPACK=ON

18

I was able to fix this by installing this package:

sudo apt-get install libtbb-dev

“make” goes further, but then I get this error message:
…
[ 86%] Building CXX object CMakeFiles/nglib.dir/nglib/nglib_occ.cpp.o
[ 87%] Linking CXX shared library libnglib.so
/usr/bin/ld: cannot find -lXi: No such file or directory
collect2: error: ld returned 1 exit status
make[8]: *** [CMakeFiles/nglib.dir/build.make:2674: libnglib.so] Error 1
make[7]: *** [CMakeFiles/Makefile2:567: CMakeFiles/nglib.dir/all] Error 2
make[6]: *** [Makefile:166: all] Error 2
make[5]: *** [CMakeFiles/netgen.dir/build.make:89: dependencies/src/netgen-stamp/netgen-build] Error 2
make[4]: *** [CMakeFiles/Makefile2:85: CMakeFiles/netgen.dir/all] Error 2
make[3]: *** [Makefile:136: all] Error 2
make[2]: *** [CMakeFiles/netgen_project.dir/build.make:86: dependencies/src/netgen_project-stamp/netgen_project-build] Error 2
make[1]: *** [CMakeFiles/Makefile2:150: CMakeFiles/netgen_project.dir/all] Error 2
make: *** [Makefile:156: all] Error 2

Any suggestions?

19

can you try something like apt-get install libXi-dev ? I guess you are missing that package somehow

20

Oh, duh. The flag " -lXi " confused me. I didn’t realize it was a library to download.

Yes, doing:

sudo apt-get -y install libxi-dev

fixed it.