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#1 2025-03-14 03:35:53

AlexBeer
Member
Registered: 2023-08-24
Posts: 22

Shared library not found: Plumed compile problem [resolved]

Hi,
I compiled plumed but the binary complains of missing library, so I run ldd with the binary as argument and found that some .so are missing:

        ldd ~/plumed-2.9.3/bin/plumed
	linux-vdso.so.1 (0x000075032ac34000)
	libplumedKernel.so => ~/plumed-2.9/lib/libplumedKernel.so (0x0000750329c00000)
	libmpi.so.40 => /usr/lib/libmpi.so.40 (0x0000750329800000)
	libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x0000750329400000)
	libm.so.6 => /usr/lib/libm.so.6 (0x000075032ab21000)
	libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x0000750329bd2000)
	libc.so.6 => /usr/lib/libc.so.6 (0x000075032920e000)
	libfftw3.so.3 => /usr/lib/libfftw3.so.3 (0x0000750328e00000)
	libgsl.so.27 => not found
	libcblas.so.3 => /usr/lib/libcblas.so.3 (0x00007503297c9000)
	libz.so.1 => /usr/lib/libz.so.1 (0x0000750329b7c000)
	liblapack.so.3 => /usr/lib/liblapack.so.3 (0x0000750327e00000)
	libblas.so.3 => /usr/lib/libblas.so.3 (0x000075032970b000)
	libnetcdf.so.19 => not found
	libtk.so => /usr/lib/libtk.so (0x00007503290c6000)
	libtcl.so => /usr/lib/libtcl.so (0x0000750328c4b000)
	libmpi_cxx.so.40 => not found
	libgomp.so.1 => /usr/lib/libgomp.so.1 (0x00007503296b8000)
	libopen-pal.so.80 => /usr/lib/libopen-pal.so.80 (0x0000750327d27000)
	libfabric.so.1 => /usr/lib/libfabric.so.1 (0x0000750327800000)
	libucp.so.0 => /usr/lib/libucp.so.0 (0x00007503276ab000)
	libucs.so.0 => /usr/lib/libucs.so.0 (0x00007503274f0000)
	libevent_core-2.1.so.7 => /usr/lib/libevent_core-2.1.so.7 (0x0000750329686000)
	libevent_pthreads-2.1.so.7 => /usr/lib/libevent_pthreads-2.1.so.7 (0x000075032ab14000)
	libhwloc.so.15 => /usr/lib/libhwloc.so.15 (0x0000750329061000)
	libpmix.so.2 => /usr/lib/libpmix.so.2 (0x0000750327200000)
	/lib64/ld-linux-x86-64.so.2 => /usr/lib64/ld-linux-x86-64.so.2 (0x000075032ac36000)
	libgfortran.so.5 => /usr/lib/libgfortran.so.5 (0x0000750326e00000)
	libXft.so.2 => /usr/lib/libXft.so.2 (0x0000750329047000)
	libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0x0000750327cd7000)
	libX11.so.6 => /usr/lib/libX11.so.6 (0x0000750326cbf000)
	libXss.so.1 => /usr/lib/libXss.so.1 (0x0000750329b77000)
	libucm.so.0 => /usr/lib/libucm.so.0 (0x0000750327cba000)
	libuct.so.0 => /usr/lib/libuct.so.0 (0x0000750327c73000)
	libnuma.so.1 => /usr/lib/libnuma.so.1 (0x0000750329b69000)
	libsframe.so.1 => /usr/lib/libsframe.so.1 (0x000075032903f000)
	libzstd.so.1 => /usr/lib/libzstd.so.1 (0x0000750326bda000)
	libudev.so.1 => /usr/lib/libudev.so.1 (0x00007503274a9000)
	libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0x0000750327136000)
	libXrender.so.1 => /usr/lib/libXrender.so.1 (0x0000750329033000)
	libexpat.so.1 => /usr/lib/libexpat.so.1 (0x0000750327c49000)
	libxcb.so.1 => /usr/lib/libxcb.so.1 (0x000075032747e000)
	libXext.so.6 => /usr/lib/libXext.so.6 (0x0000750327469000)
	libcap.so.2 => /usr/lib/libcap.so.2 (0x0000750327c3d000)
	libbz2.so.1.0 => /usr/lib/libbz2.so.1.0 (0x0000750327456000)
	libpng16.so.16 => /usr/lib/libpng16.so.16 (0x000075032741c000)
	libharfbuzz.so.0 => /usr/lib/libharfbuzz.so.0 (0x0000750326ab5000)
	libbrotlidec.so.1 => /usr/lib/libbrotlidec.so.1 (0x0000750327127000)
	libXau.so.6 => /usr/lib/libXau.so.6 (0x0000750327417000)
	libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x0000750326aad000)
	libglib-2.0.so.0 => /usr/lib/libglib-2.0.so.0 (0x0000750326955000)
	libgraphite2.so.3 => /usr/lib/libgraphite2.so.3 (0x0000750326933000)
	libbrotlicommon.so.1 => /usr/lib/libbrotlicommon.so.1 (0x0000750326910000)
	libpcre2-8.so.0 => /usr/lib/libpcre2-8.so.0 (0x0000750326864000)

but they are just outdated:

        sudo ldconfig -p | grep libgsl
	libgsl.so.28 (libc6,x86-64) => /usr/lib/libgsl.so.28
	libgsl.so (libc6,x86-64) => /usr/lib/libgsl.so

The configure prompt is:

./configure CC=mpicc CXX=mpicxx --disable-external-molfile-plugins --prefix=~/plumed-2.9.3 --enable-modules=all PYTHON_BIN=python3 CPPFLAGS="" LDFLAGS="-lnetcdf -ltk -ltcl -lgsl -lgslcblas -lm"

Any suggestions?

Best Regards

Last edited by AlexBeer (2025-03-19 17:34:32)

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#2 2025-03-14 03:47:14

mackin_cheese
Member
Registered: 2025-01-07
Posts: 459

Re: Shared library not found: Plumed compile problem [resolved]

did you compile from source or did you build from an AUR package?

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#3 2025-03-14 03:51:18

Scimmia
Fellow
Registered: 2012-09-01
Posts: 12,638

Re: Shared library not found: Plumed compile problem [resolved]

Start off by using lddtree from the pax-utils package to see where your actual problem is. It may or may not be plumbed

Things can't be linked to libraries that don't exist. Either this is an old build, or it's a partial update situation.

Last edited by Scimmia (2025-03-14 03:52:15)

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#4 2025-03-14 10:23:55

seth
Member
Registered: 2012-09-03
Posts: 63,326

Re: Shared library not found: Plumed compile problem [resolved]

LDFLAGS="-lnetcdf -ltk -ltcl -lgsl -lgslcblas -lm"

gsl and netcdf currently cannot be resolved, so either you didn't rebuild plumed after those were updated or the rebuild attempt failed/fails.

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#5 2025-03-14 14:08:40

AlexBeer
Member
Registered: 2023-08-24
Posts: 22

Re: Shared library not found: Plumed compile problem [resolved]

mackin_cheese wrote:

did you compile from source or did you build from an AUR package?

from source

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#6 2025-03-14 14:19:35

AlexBeer
Member
Registered: 2023-08-24
Posts: 22

Re: Shared library not found: Plumed compile problem [resolved]

seth wrote:

LDFLAGS="-lnetcdf -ltk -ltcl -lgsl -lgslcblas -lm"

gsl and netcdf currently cannot be resolved, so either you didn't rebuild plumed after those were updated or the rebuild attempt failed/fails.

I run " rm -r ~/plumed-2.9.3/*" to be sure that what is build is installed, and make clean before each build.

Only oddity is the dependence on older plumed library

libplumedKernel.so => ~/plumed-2.9/lib/libplumedKernel.so (0x00007ed855e00000)

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#7 2025-03-14 14:41:27

WorMzy
Administrator
From: Scotland
Registered: 2010-06-16
Posts: 12,743
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Re: Shared library not found: Plumed compile problem [resolved]

Mod note: Moving to AUR Issues.

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#8 2025-03-14 15:00:48

seth
Member
Registered: 2012-09-03
Posts: 63,326

Re: Shared library not found: Plumed compile problem [resolved]

Only oddity is the dependence on older plumed library

Well, try to rebuild that resp. indeed check the lddtree to see where the dependency is coming from.

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#9 2025-03-19 17:29:37

AlexBeer
Member
Registered: 2023-08-24
Posts: 22

Re: Shared library not found: Plumed compile problem [resolved]

Ok, thanks. I have to remove "PLUMED_KERNEL" env variable which point to "/home/myuser/plumed-2.9/lib/libplumedKernel.so" before compile. In fact lddtree show deps of "libplumedKernel.so" upon "libgsl.so":

libplumedKernel.so => /home/myuser/plumed-2.9.3/lib/libplumedKernel.so
        libfftw3.so.3 => /usr/lib/libfftw3.so.3
        libgsl.so.28 => /usr/lib/libgsl.so.28
        libcblas.so.3 => /usr/lib/libcblas.so.3
        liblapack.so.3 => /usr/lib/liblapack.so.3
        libblas.so.3 => /usr/lib/libblas.so.3
        libgomp.so.1 => /usr/lib/libgomp.so.1

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#10 2025-03-19 17:32:17

mackin_cheese
Member
Registered: 2025-01-07
Posts: 459

Re: Shared library not found: Plumed compile problem [resolved]

AlexBeer wrote:
mackin_cheese wrote:

did you compile from source or did you build from an AUR package?

from source

Is there a reason why you're building from source instead of the AUR?

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