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liblapack.so.3 issue

https://www3.aps.anl.gov/forums/elegant/viewtopic.php?f=11&t=1486

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liblapack.so.3 issue

Posted: 16 Oct 2026, 07:54
by Skamarokha
Good day!

Run into the issue with libraries on elegant execution.
elegant: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory
Used preferred installation steps from guide for Ubuntu 26.04. Installed mpich version of elegant 2026.3.0. Please, help troubleshoot.

Re: liblapack.so.3 issue

Posted: 16 Oct 2026, 09:29
by soliday
Hello Mikhail,

Please try:

sudo apt install liblapack3

If the error persists, please post the output of:

command -v elegant
dpkg-query -W liblapack3
ldd "$(command -v elegant)"

--Bob

Re: liblapack.so.3 issue

Posted: 17 Oct 2026, 23:34
by Skamarokha
Hello, Bob

Installing liblapack3 seem to work for elegant, but Pelegant won't run as expected. Running Pelegant holds terminal and produces no output.

Re: liblapack.so.3 issue

Posted: 18 Oct 2026, 07:22
by soliday
Here is the command to install all the dependencies you will need if you don't already have them installed on Ubuntu 26.04:

sudo apt update
sudo apt install \
mpich libmpich12 \
liblapack3 libblas3 libfftw3-double3 \
liblzma5 zlib1g \
libgfortran5 libgomp1 \
libstdc++6 libgcc-s1 libc6

Re: liblapack.so.3 issue

Posted: 18 Oct 2026, 07:33
by Skamarokha
Mentioned packages are already installed.
soliday wrote: ↑
18 Oct 2026, 07:22
 mpich libmpich12 \
liblapack3 libblas3 libfftw3-double3 \
liblzma5 zlib1g \
libgfortran5 libgomp1 \
libstdc++6 libgcc-s1 libc6

Re: liblapack.so.3 issue

Posted: 18 Oct 2026, 07:45
by soliday
Hello Mikhail,

Thanks for checking. Please post the exact command you use to launch Pelegant and the output of:

Code: Select all

type -a Pelegant mpiexec mpiexec.mpich
mpichversion
ldd "$(command -v Pelegant)"
Then please try these two tests separately:

Code: Select all

MPIEXEC_TIMEOUT=20 mpiexec.mpich -n 2 /bin/hostname
This should print your hostname twice. It checks whether the MPI launcher can start processes.

Code: Select all

MPIEXEC_TIMEOUT=20 mpiexec.mpich -n 2 Pelegant
This deliberately supplies no input file. Pelegant should print its greeting and usage information, then exit. It lets us check startup independently of your simulation.

The MPIEXEC_TIMEOUT setting limits each test to 20 seconds. Please post the complete output and indicate whether either test times out.

--Bob

Re: liblapack.so.3 issue

Posted: 18 Oct 2026, 08:12
by Skamarokha
I ran Pelegant without input file to test it as follows
mpiexec -n 2 Pelegant
The output of first command is
type -a Pelegant mpiexec mpiexec.mpich
mpichversion
ldd "$(command -v Pelegant)"
Pelegant is /usr/bin/Pelegant
Pelegant is /bin/Pelegant
mpiexec is /usr/bin/mpiexec
mpiexec is /bin/mpiexec
mpiexec.mpich is /usr/bin/mpiexec.mpich
mpiexec.mpich is /bin/mpiexec.mpich
MPICH Version: 4.3.2
MPICH Release date: Mon Oct 6 11:14:20 AM CDT 2025
MPICH ABI: 17:2:5
MPICH Device: ch4:ucx
MPICH configure: --build=x86_64-linux-gnu --prefix=/usr --includedir=${prefix}/include --mandir=${prefix}/share/man --infodir=${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-ibverbs --with-libfabric=/usr --with-slurm=/usr --with-ucx=/usr --with-device=ch4:ucx --with-pm=hydra --with-hwloc-prefix=/usr --with-wrapper-dl-type=none --enable-shared --without-yaksa --prefix=/usr --enable-fortran=all --disable-rpath --disable-wrapper-rpath --sysconfdir=/etc/mpich --libdir=${prefix}/lib/x86_64-linux-gnu/mpich/lib --includedir=${prefix}/lib/x86_64-linux-gnu/mpich/include --docdir=/usr/share/doc/mpich CPPFLAGS= CFLAGS= CXXFLAGS= FFLAGS=-O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -fcf-protection -fdebug-prefix-map=/build/mpich-f8z5Zh/mpich-4.3.2=/usr/src/mpich-4.3.2-2 -fallow-invalid-boz -fallow-argument-mismatch FCFLAGS=-O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -fcf-protection -fdebug-prefix-map=/build/mpich-f8z5Zh/mpich-4.3.2=/usr/src/mpich-4.3.2-2 -fallow-invalid-boz -fallow-argument-mismatch BASH_SHELL=/bin/bash
MPICH CC: gcc -g -O2 -Werror=implicit-function-declaration -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/mpich-f8z5Zh/mpich-4.3.2=/usr/src/mpich-4.3.2-2 -O2
MPICH CXX: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/mpich-f8z5Zh/mpich-4.3.2=/usr/src/mpich-4.3.2-2 -O2
MPICH F77: gfortran -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -fcf-protection -fdebug-prefix-map=/build/mpich-f8z5Zh/mpich-4.3.2=/usr/src/mpich-4.3.2-2 -fallow-invalid-boz -fallow-argument-mismatch -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -fcf-protection -fdebug-prefix-map=/build/mpich-f8z5Zh/mpich-4.3.2=/usr/src/mpich-4.3.2-2 -cpp -fallow-invalid-boz -fallow-argument-mismatch -O2
MPICH FC: gfortran -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -fcf-protection -fdebug-prefix-map=/build/mpich-f8z5Zh/mpich-4.3.2=/usr/src/mpich-4.3.2-2 -fallow-invalid-boz -fallow-argument-mismatch -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -fcf-protection -fdebug-prefix-map=/build/mpich-f8z5Zh/mpich-4.3.2=/usr/src/mpich-4.3.2-2 -cpp -fallow-invalid-boz -fallow-argument-mismatch -O2
MPICH features: threadcomm

linux-vdso.so.1 (0x00007ae5275cf000)
liblzma.so.5 => /usr/lib/x86_64-linux-gnu/liblzma.so.5 (0x00007ae52757f000)
libz.so.1 => /usr/lib/x86_64-linux-gnu/libz.so.1 (0x00007ae527561000)
libfftw3.so.3 => /usr/lib/x86_64-linux-gnu/libfftw3.so.3 (0x00007ae526a00000)
liblapack.so.3 => /usr/lib/x86_64-linux-gnu/liblapack.so.3 (0x00007ae526200000)
libblas.so.3 => /usr/lib/x86_64-linux-gnu/libblas.so.3 (0x00007ae5274ac000)
libmpich.so.12 => /usr/lib/x86_64-linux-gnu/libmpich.so.12 (0x00007ae525600000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007ae525200000)
libm.so.6 => /usr/lib/x86_64-linux-gnu/libm.so.6 (0x00007ae526cda000)
libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007ae52744b000)
libc.so.6 => /usr/lib/x86_64-linux-gnu/libc.so.6 (0x00007ae524e00000)
libgfortran.so.5 => /usr/lib/x86_64-linux-gnu/libgfortran.so.5 (0x00007ae524a00000)
libmvec.so.1 => /usr/lib/x86_64-linux-gnu/libmvec.so.1 (0x00007ae526105000)
libgcc_s.so.1 => /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007ae52741b000)
libhwloc.so.15 => /usr/lib/x86_64-linux-gnu/libhwloc.so.15 (0x00007ae526c75000)
libucp.so.0 => /usr/lib/x86_64-linux-gnu/libucp.so.0 (0x00007ae525088000)
libucs.so.0 => /usr/lib/x86_64-linux-gnu/libucs.so.0 (0x00007ae526990000)
/lib64/ld-linux-x86-64.so.2 (0x00007ae5275d1000)
libudev.so.1 => /usr/lib/x86_64-linux-gnu/libudev.so.1 (0x00007ae526c2e000)
libuct.so.0 => /usr/lib/x86_64-linux-gnu/libuct.so.0 (0x00007ae526946000)
libucm.so.0 => /usr/lib/x86_64-linux-gnu/libucm.so.0 (0x00007ae526929000)
First test:
(base) john@s1-33-skamarokh2:~$ MPIEXEC_TIMEOUT=20 mpiexec.mpich -n 2 /bin/hostname
s1-33-skamarokh2
s1-33-skamarokh2
Second test:
(base) john@s1-33-skamarokh2:~$ MPIEXEC_TIMEOUT=20 mpiexec.mpich -n 2 Pelegant
[mpiexec@s1-33-skamarokh2] APPLICATION TIMED OUT, TIMEOUT = 20s

Re: liblapack.so.3 issue

Posted: 18 Oct 2026, 08:29
by soliday
Can you show me the output of this command:

Code: Select all

UCX_TLS=tcp,self UCX_LOG_LEVEL=info MPIEXEC_TIMEOUT=20 \
  /usr/bin/mpiexec.mpich -n 2 /usr/bin/Pelegant
I will have more time tomorrow to try to see if I can duplicate the problem on one of my computers.

--Bob

Re: liblapack.so.3 issue

Posted: 18 Oct 2026, 08:33
by Skamarokha
soliday wrote: ↑
18 Oct 2026, 08:29
 Can you show me the output of this command:
(base) john@s1-33-skamarokh2:~$ UCX_TLS=tcp,self UCX_LOG_LEVEL=info MPIEXEC_TIMEOUT=20 \
/usr/bin/mpiexec.mpich -n 2 /usr/bin/Pelegant
[mpiexec@s1-33-skamarokh2] APPLICATION TIMED OUT, TIMEOUT = 20s
soliday wrote: ↑
18 Oct 2026, 08:29
 I will have more time tomorrow
Sure.

Re: liblapack.so.3 issue

Posted: 02 Nov 2026, 13:34
by Skamarokha
Bob,

In the absence of better solution I have removed mpich version of elegant and installed openmpi with openmpi version of elegant. Both elegant and pelegant work as expected now.

Also, guide page for linux refers to previous versions of elegant (2026.3.0).
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