Transitioning from IBAMR 0.8 to 0.16

[hoover.a...@gmail.com]

Hi all,

I am currently transitioning from using IBAMR 0.8.0 to 0.16 that was installed using autoIBAMR. I previously had a module installed for this by the cluster's IT staff, but they are having difficulty navigating the new installation (I believe due to CMake).

Currently, it looks like it's compiling fine (though the CMakeCache may say otherwise, attached), but attempting to run it I get the following error:

./main3d: error while loading shared libraries: libpetsc.so.3.23: cannot open shared object file: No such file or directory

Any hints?

Best,

Alex

  

[Wells, David]

Hi Alex,

That error indicates that the application is linked against a copy of PETSc which no longer exists. If you run

ldd main3d

what do you see? Can you check if there is a copy of PETSc installed in that location? It may also be illuminating to run the same command on libIBTK2d.so.

Best,

David

---

From: ibamr...@googlegroups.com <ibamr...@googlegroups.com> on behalf of hoover.a...@gmail.com <hoover.a...@gmail.com>
Sent: Tuesday, October 21, 2025 5:29 PM
To: IBAMR Users <ibamr...@googlegroups.com>
Subject: [ibamr-users] Transitioning from IBAMR 0.8 to 0.16

 

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[hoover.a...@gmail.com]

For this second command, it was not found. For the first command:

[hooverap@pitzer-login03 newattempt]$ ldd main3d

linux-vdso.so.1 (0x00007ffc79bcc000)

libpetsc.so.3.23 => not found

libmesh_opt.so.0 => not found

libtimpi_opt.so.5 => not found

libhdf5hl_fortran.so.200 => /lib64/libhdf5hl_fortran.so.200 (0x0000152d0faef000)

libhdf5_fortran.so.200 => /lib64/libhdf5_fortran.so.200 (0x0000152d0fa95000)

libhdf5_cpp.so.200 => /lib64/libhdf5_cpp.so.200 (0x0000152d0fa1c000)

libhdf5.so.200 => /lib64/libhdf5.so.200 (0x0000152d0f623000)

libIBAMR3d.so => not found

libIBTK3d.so => not found

libmpicxx.so.12 => /apps/spack/0.21/pitzer/linux-rhel9-skylake/mvapich/gcc/12.3.0/3.0-g3ki46b/lib/libmpicxx.so.12 (0x0000152d0f5fc000)

libmpi.so.12 => /apps/spack/0.21/pitzer/linux-rhel9-skylake/mvapich/gcc/12.3.0/3.0-g3ki46b/lib/libmpi.so.12 (0x0000152d0e508000)

libstdc++.so.6 => /apps/spack/0.21/pitzer/linux-rhel9-skylake/gcc/gcc/11.4.1/12.3.0-3kyf2vj/lib64/libstdc++.so.6 (0x0000152d0e2de000)

libm.so.6 => /lib64/libm.so.6 (0x0000152d0e201000)

libgcc_s.so.1 => /apps/spack/0.21/pitzer/linux-rhel9-skylake/gcc/gcc/11.4.1/12.3.0-3kyf2vj/lib64/libgcc_s.so.1 (0x0000152d0e1e0000)

libc.so.6 => /lib64/libc.so.6 (0x0000152d0dfd7000)

libhdf5_hl.so.200 => /lib64/libhdf5_hl.so.200 (0x0000152d0dfb3000)

libgfortran.so.5 => /apps/spack/0.21/pitzer/linux-rhel9-skylake/gcc/gcc/11.4.1/12.3.0-3kyf2vj/lib64/libgfortran.so.5 (0x0000152d0dce0000)

libsz.so.2 => /lib64/libsz.so.2 (0x0000152d0dcd4000)

libz.so.1 => /lib64/libz.so.1 (0x0000152d0dcba000)

libudev.so.1 => /lib64/libudev.so.1 (0x0000152d0dc89000)

libpciaccess.so.0 => /apps/spack/0.21/pitzer/linux-rhel9-skylake/libpciaccess/gcc/12.3.0/0.17-jl6kb22/lib/libpciaccess.so.0 (0x0000152d0dc7d000)

libOpenCL.so.1 => /apps/spack/0.21/pitzer/linux-rhel9-skylake/intel-oneapi-compilers/gcc/11.4.1/2023.2.3-xq4aqvz/compiler/2023.2.3/linux/lib/libOpenCL.so.1 (0x0000152d0dc69000)

libxml2.so.2 => /apps/spack/0.21/pitzer/linux-rhel9-skylake/libxml2/gcc/12.3.0/2.10.3-peqyldo/lib/libxml2.so.2 (0x0000152d0db04000)

libucp.so.0 => /apps/hpcx/2.17.1/ucx/mt/lib/libucp.so.0 (0x0000152d0da25000)

libucs.so.0 => /apps/hpcx/2.17.1/ucx/mt/lib/libucs.so.0 (0x0000152d0d89d000)

libgpfs.so => /lib64/libgpfs.so (0x0000152d0d687000)

libpmi.so.0 => /lib64/libpmi.so.0 (0x0000152d0d67f000)

/lib64/ld-linux-x86-64.so.2 (0x0000152d0fb43000)

libquadmath.so.0 => /apps/spack/0.21/pitzer/linux-rhel9-skylake/gcc/gcc/11.4.1/12.3.0-3kyf2vj/lib64/libquadmath.so.0 (0x0000152d0d636000)

libdl.so.2 => /lib64/libdl.so.2 (0x0000152d0d62f000)

libsvml.so => /apps/spack/0.21/pitzer/linux-rhel9-skylake/intel-oneapi-compilers/gcc/11.4.1/2023.2.3-xq4aqvz/compiler/2023.2.3/linux/compiler/lib/intel64_lin/libsvml.so (0x0000152d0bf55000)

libirng.so => /apps/spack/0.21/pitzer/linux-rhel9-skylake/intel-oneapi-compilers/gcc/11.4.1/2023.2.3-xq4aqvz/compiler/2023.2.3/linux/compiler/lib/intel64_lin/libirng.so (0x0000152d0bc3c000)

libimf.so => /apps/spack/0.21/pitzer/linux-rhel9-skylake/intel-oneapi-compilers/gcc/11.4.1/2023.2.3-xq4aqvz/compiler/2023.2.3/linux/compiler/lib/intel64_lin/libimf.so (0x0000152d0b845000)

libintlc.so.5 => /apps/spack/0.21/pitzer/linux-rhel9-skylake/intel-oneapi-compilers/gcc/11.4.1/2023.2.3-xq4aqvz/compiler/2023.2.3/linux/compiler/lib/intel64_lin/libintlc.so.5 (0x0000152d0b7c8000)

libpthread.so.0 => /lib64/libpthread.so.0 (0x0000152d0b7c1000)

liblzma.so.5 => /apps/spack/0.21/pitzer/linux-rhel9-skylake/xz/gcc/12.3.0/5.4.1-nkm37ne/lib/liblzma.so.5 (0x0000152d0b792000)

libiconv.so.2 => /apps/spack/0.21/pitzer/linux-rhel9-skylake/libiconv/gcc/12.3.0/1.17-bcgrlj2/lib/libiconv.so.2 (0x0000152d0b685000)

libuct.so.0 => /apps/hpcx/2.17.1/ucx/mt/lib/libuct.so.0 (0x0000152d0b64b000)

libucm.so.0 => /apps/hpcx/2.17.1/ucx/mt/lib/libucm.so.0 (0x0000152d0b62f000)

libslurm_pmi.so => /usr/lib64/slurm/libslurm_pmi.so (0x0000152d0b42d000)

libresolv.so.2 => /lib64/libresolv.so.2 (0x0000152d0b419000)

I know that some of the other locations are:

export IBAMR_DIR=/apps/project/pbs0334/ibamr/gcc/12.3/mvapich/3.0/0.16/packages/IBAMR-0.16.0
export LIBMESH_DIR=/apps/project/pbs0334/ibamr/gcc/12.3/mvapich/3.0/0.16/packages/libmesh-1.7.8
export SAMRAI_DIR=/apps/project/pbs0334/ibamr/gcc/12.3/mvapich/3.0/0.16/packages/IBSAMRAI2-2025.01.09
export PETSC_DIR=/apps/project/pbs0334/ibamr/gcc/12.3/mvapich/3.0/0.16/packages/petsc-3.23.3
export HDF5_DIR=/apps/project/pbs0334/ibamr/gcc/12.3/mvapich/3.0/0.16/packages/hdf5-1.12.2
export MPI_DIR=/apps/spack/0.21/pitzer/linux-rhel9-skylake/mvapich/gcc/12.3.0/3.0-g3ki46b

[Wells, David]

Hi Alex,

It looks like most of the libraries installed by autoibamr which this app should depend on were deleted after it was installed. Furthermore, I see that it is linked against both GCC 11 and GCC 12 libraries - that can't be right.

Can you check if autoibamr installed IBAMR, libMesh, etc. in the place you think it did? I suspect it has been moved or deleted. You'll probably need to rerun autoibamr with one set of MPI compiler wrappers to ensure things don't get mixed up.

If your system administrator has questions about IBAMR feel free to have them email me (or respond in this thread).

Best,

David

---

From: ibamr...@googlegroups.com <ibamr...@googlegroups.com> on behalf of hoover.a...@gmail.com <hoover.a...@gmail.com>

Sent: Wednesday, October 22, 2025 12:25 PM
To: IBAMR Users <ibamr...@googlegroups.com>
Subject: Re: [ibamr-users] Transitioning from IBAMR 0.8 to 0.16

 

To view this discussion visit https://groups.google.com/d/msgid/ibamr-users/7d6a2830-32ba-4e8c-9ef1-995d1854c5a6n%40googlegroups.com.