Error: cannot find -lmkl_intel_lp64 while compiling on Ubuntu 20.04

Ubuntu 20 is escalating positions as the heir of CentOS 7, and I started experiencing compatibility issues. I was compiling relion with the next options

cmake -DAMDFFTW=ON -DCUDA_ARCH=86 -DCUDA=ON -DCudaTexture=ON 
-DFORCE_OWN_FLTK=ON -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc
-DMPI_C_COMPILER=/usr/bin/mpicc 
-DMPI_C_LIBRARIES=/usr/lib/x86_64-linux-gnu/openmpi/lib/ 
-DMPI_C_INCLUDE_PATH=/usr/lib/x86_64-linux-gnu/openmpi/include/ 
-DCUDA_ARCH=61 -DCUDA=ON -DCudaTexture=ON -DMKLFFT=ON 
-DFORCE_OWN_FLTK=ON -DGUI=ON 
-DCMAKE_INSTALL_PREFIX=/XXX/relion_local/ 
-D CMAKE_BUILD_TYPE=Release ..

when I found this error

[ 59%] Linking CXX executable ../../bin/relion_tomo_tomo_ctf
/usr/bin/ld: cannot find -lmkl_intel_lp64
/usr/bin/ld: cannot find -lmkl_sequential
/usr/bin/ld: cannot find -lmkl_core
collect2: error: ld returned 1 exit status
make[2]: *** [src/apps/CMakeFiles/tomo_ctf.dir/build.make:102: 
bin/relion_tomo_tomo_ctf] Error 1
make[1]: *** [CMakeFiles/Makefile2:352: 
src/apps/CMakeFiles/tomo_ctf.dir/all] Error 2
make: *** [Makefile:130: all] Error 2

I’m using the default package install locations, no modules or anything fancy. So it looks like some libraries are missing. Of course I try to find them with ldconfig -p | grep ‘mkl’ but they are obviously not there. Let’s install them:

# apt-get install libmkl*intel* libmkl*se* libmkl*core*
Reading package lists... Done
Building dependency tree 
Reading state information... Done
Note, selecting 'libmkl-intel-thread' for glob 'libmkl*intel*'
Note, selecting 'libmkl-blacs-intelmpi-ilp64' for glob 'libmkl*intel*'
Note, selecting 'libmkl-intel-ilp64' for glob 'libmkl*intel*'
Note, selecting 'libmkl-blacs-intelmpi-lp64' 
for glob 'libmkl*intel*'
Note, selecting 'libmkl-intel-lp64' for glob 'libmkl*intel*'
Note, selecting 'libmkl-sequential' for glob 'libmkl*se*'
Note, selecting 'libmkl-core' for glob 'libmkl*core*'
Note, selecting 'libmkl-cdft-core' for glob 'libmkl*core*'
The following additional packages will be installed:
libmkl-def libmkl-locale libmkl-vml-def
The following NEW packages will be installed:
libmkl-blacs-intelmpi-ilp64 libmkl-blacs-intelmpi-lp64 
libmkl-cdft-core libmkl-core libmkl-def 
libmkl-intel-ilp64 libmkl-intel-lp64 
libmkl-intel-thread libmkl-locale 
libmkl-sequential libmkl-vml-def
0 upgraded, 11 newly installed, 0 to remove and 19 not upgraded.
Need to get 38,4 MB of archives.
After this operation, 204 MB of additional disk space will be used.
Do you want to continue? [Y/n] y

You may need to run apt-get install mklibs in addition. Of course it depends on what you have been doing with your system so far, since this will call some python libraries also. After getting those packages, make and make install run without errors. Time to ask the user to test it…

ERROR : /usr/share/Modules/init/sh: No such file or directory on Ubuntu 22.04

We started the migration to a new Linux flavour – in principle Ubuntu– and therefore we started also to experience the first issues. We have a very established software module method, with the module definitions being loaded from a network location. We can install software modules, but after every folder needed and every other adjustment is made we see this:

$ > ssh user@new-server
Last login: DATE from other-server.org
-bash: /usr/share/Modules/init/sh: No such file or directory

I have a machine “other-server” to check how the modules are working. And I find that the folder “Modules” is missing in Ubuntu. The content of the folder modules in the same location seems to be the same, so I do

root@new-server:/usr/share# ln -s /usr/share/modules Modules

And try logging again. With this result:

$ > ssh user@new-server
user@new-server's password: 
Last login: DATE from other-server.org
user@new-server ~ $ > module avail
/PATH/modulecmd: 
error while loading shared libraries: 
libtcl8.5.so: cannot open shared object file: 
No such file or directory

So there’s now a library problem. Let’s try to fix it very quickly. I localize a similar library

root@new-server:~# ls /usr/lib/*/*libtcl*
/usr/lib/x86_64-linux-gnu/libtcl8.6.so 
/usr/lib/x86_64-linux-gnu/libtcl8.6.so.0 
/usr/lib/x86_64-linux-gnu/libtclenvmodules.so
root@new-server:~# 
cp /usr/lib/x86_64-linux-gnu/libtcl8.6.so /usr/lib/libtcl8.5.so
root@new-server:~# ldconfig

And the error is gone. We can do this because the libraries are not so different…. I have no idea of the side effects. Let’s hope there are not so many 😉!