Comments (11)
It looks like something is not linking properly; do you have the config.log file generated when you ran configure
?
from netcdf-c.
It looks like something is not linking properly; do you have the config.log file generated when you ran
configure
?
Hi Ward,
Thanks very much for the helps, I appended the whole file of 'config.log' generated during config process.
config.log
from netcdf-c.
It looks like the instruction to link against libhdf5
is somehow not being passed along when building the tests as part of make check
. Can you provide the output from ldd liblib/.libs/libnetcdf.so
? Also, you might try this from the command line when running make check
:
$ LIBS="-lhdf5 -lhdf5_hl" make check
from netcdf-c.
It looks like the instruction to link against
libhdf5
is somehow not being passed along when building the tests as part ofmake check
. Can you provide the output fromldd liblib/.libs/libnetcdf.so
? Also, you might try this from the command line when runningmake check
:$ LIBS="-lhdf5 -lhdf5_hl" make check
Thanks very much for the reply.
This weekend I won't be able to go to the lab due to other commitments, but I will append the file: libnetcdf.so
and try out your suggestion on Monday as soon as possible. Thanks for the helps.
from netcdf-c.
It looks like the instruction to link against
libhdf5
is somehow not being passed along when building the tests as part ofmake check
. Can you provide the output fromldd liblib/.libs/libnetcdf.so
? Also, you might try this from the command line when runningmake check
:$ LIBS="-lhdf5 -lhdf5_hl" make check
Hi Ward,
I tried to run ldd liblib/.libs/libnetcdf.so
, but the address seems different on my machine, so I locate
the libnetcdf.so
file, and there are multiple files :
jin@KUKAI:~$ locate libnetcdf.so
/usr/lib/libnetcdf.so
/usr/lib/libnetcdf.so.19
/usr/lib/x86_64-linux-gnu/libnetcdf.so
/usr/lib/x86_64-linux-gnu/libnetcdf.so.19
/usr/lib/x86_64-linux-gnu/netcdf/mpi/libnetcdf.so
/usr/local/MATLAB/R2018b/bin/glnxa64/libnetcdf.so.7
/usr/local/MATLAB/R2018b/bin/glnxa64/libnetcdf.so.7.2.0
/usr/local/MATLAB/R2019a/bin/glnxa64/libnetcdf.so.13
/usr/local/MATLAB/R2019a/bin/glnxa64/libnetcdf.so.13.1.1
/usr/local/src/netcdf-c-4.9.2/lib/libnetcdf.so
/usr/local/src/netcdf-c-4.9.2/lib/libnetcdf.so.19
/usr/local/src/netcdf-c-4.9.2/lib/libnetcdf.so.19.2.2
I'm not sure which one should I run the ldd
on, I assumed /usr/local/src/netcdf-c-4.9.2/lib/libnetcdf.so
is the correct one and run ldd
on it :
ldd /usr/local/src/netcdf-c-4.9.2/lib/libnetcdf.so
linux-vdso.so.1 (0x00007ffff71ec000)
libimf.so => not found
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007feb2c44e000)
libsz.so.2 => /usr/local/lib/libsz.so.2 (0x00007feb2c439000)
libxml2.so.2 => /lib/x86_64-linux-gnu/libxml2.so.2 (0x00007feb2c257000)
libcurl.so.4 => /lib/x86_64-linux-gnu/libcurl.so.4 (0x00007feb2c1b0000)
libsvml.so => not found
libirng.so => not found
libintlc.so.5 => not found
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007feb2be00000)
/lib64/ld-linux-x86-64.so.2 (0x00007feb2c72b000)
libicuuc.so.70 => /lib/x86_64-linux-gnu/libicuuc.so.70 (0x00007feb2bc05000)
libz.so.1 => /usr/local/lib/libz.so.1 (0x00007feb2c190000)
liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007feb2c163000)
libnghttp2.so.14 => /lib/x86_64-linux-gnu/libnghttp2.so.14 (0x00007feb2c139000)
libidn2.so.0 => /lib/x86_64-linux-gnu/libidn2.so.0 (0x00007feb2c118000)
librtmp.so.1 => /lib/x86_64-linux-gnu/librtmp.so.1 (0x00007feb2c0f9000)
libssh.so.4 => /lib/x86_64-linux-gnu/libssh.so.4 (0x00007feb2c08c000)
libpsl.so.5 => /lib/x86_64-linux-gnu/libpsl.so.5 (0x00007feb2c078000)
libssl.so.3 => /lib/x86_64-linux-gnu/libssl.so.3 (0x00007feb2bb61000)
libcrypto.so.3 => /lib/x86_64-linux-gnu/libcrypto.so.3 (0x00007feb2b600000)
libgssapi_krb5.so.2 => /lib/x86_64-linux-gnu/libgssapi_krb5.so.2 (0x00007feb2bb0d000)
libldap-2.5.so.0 => /lib/x86_64-linux-gnu/libldap-2.5.so.0 (0x00007feb2baae000)
liblber-2.5.so.0 => /lib/x86_64-linux-gnu/liblber-2.5.so.0 (0x00007feb2c065000)
libzstd.so.1 => /lib/x86_64-linux-gnu/libzstd.so.1 (0x00007feb2b531000)
libbrotlidec.so.1 => /lib/x86_64-linux-gnu/libbrotlidec.so.1 (0x00007feb2c055000)
libicudata.so.70 => /lib/x86_64-linux-gnu/libicudata.so.70 (0x00007feb29800000)
libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007feb29400000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007feb2c035000)
libunistring.so.2 => /lib/x86_64-linux-gnu/libunistring.so.2 (0x00007feb29656000)
libgnutls.so.30 => /lib/x86_64-linux-gnu/libgnutls.so.30 (0x00007feb29215000)
libhogweed.so.6 => /lib/x86_64-linux-gnu/libhogweed.so.6 (0x00007feb2ba66000)
libnettle.so.8 => /lib/x86_64-linux-gnu/libnettle.so.8 (0x00007feb2b4eb000)
libgmp.so.10 => /lib/x86_64-linux-gnu/libgmp.so.10 (0x00007feb2b469000)
libkrb5.so.3 => /lib/x86_64-linux-gnu/libkrb5.so.3 (0x00007feb2914a000)
libk5crypto.so.3 => /lib/x86_64-linux-gnu/libk5crypto.so.3 (0x00007feb2b43a000)
libcom_err.so.2 => /lib/x86_64-linux-gnu/libcom_err.so.2 (0x00007feb2c02b000)
libkrb5support.so.0 => /lib/x86_64-linux-gnu/libkrb5support.so.0 (0x00007feb2ba58000)
libsasl2.so.2 => /lib/x86_64-linux-gnu/libsasl2.so.2 (0x00007feb2b41f000)
libbrotlicommon.so.1 => /lib/x86_64-linux-gnu/libbrotlicommon.so.1 (0x00007feb29633000)
libp11-kit.so.0 => /lib/x86_64-linux-gnu/libp11-kit.so.0 (0x00007feb2900f000)
libtasn1.so.6 => /lib/x86_64-linux-gnu/libtasn1.so.6 (0x00007feb28ff7000)
libkeyutils.so.1 => /lib/x86_64-linux-gnu/libkeyutils.so.1 (0x00007feb2ba51000)
libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007feb28fe3000)
libffi.so.8 => /lib/x86_64-linux-gnu/libffi.so.8 (0x00007feb2ba44000)
from netcdf-c.
And also I retried the make check
with your suggestion $ LIBS="-lhdf5 -lhdf5_hl" make check
, but I still got errors that looks similar compare to previous time :
LIBS="-lhdf5 -lhdf5_hl make check.txt
from netcdf-c.
You'll want to run ldd
against the copy of libnetcdf.so
you are compiling; it won't be any of the versions generated and distributed by other packages. After compiling, it typically resides in the netcdf-c/liblib/.libs
directory; sorry for not being more specific. You'll want to look in the folder you are compiling in, and then it will be liblib/.libs
from netcdf-c.
Thanks very much for the reply.
I rechecked the directories and this is the directory where I install/ compiled netcdf : /usr/local/src/netcdf-c-4.9.2/
,
And from the image, there is no dir named 'liblib', but has a 'lib' dir. And inside 'lib' dir there is a file named libnetcdf.so
:
On the other hands, I checked the directory where I downloaded netcdf: /home/jin/Downloads/netcdf-c-4.9.2/
:
And inside this, there is a dir named 'liblib', so I also checked it, but there is no libnetcdf.so
inside:
So as a conclusion, did I made some mistakes or the libnetcdf.so
from /usr/local/src/netcdf-c-4.9.2/lib/
should be the correct one maybe? Here is the information after I run ldd
against that file :
ldd_info.txt
from netcdf-c.
This is very peculiar; your build system is finding libhdf5
, and purports to be linking against it (from the config.log file you provided). But the ldd
output you provided shows no link to it. Can you share the contents of ${H5DIR}/lib
? Also, can you share the output if you run /usr/local/src/netcdf-c-4.9.2/nc-config --libs
and /usr/local/src/netcdf-c-4.9.2/nc-config --all
?
from netcdf-c.
Sorry for being late, we found out someone accidentally deleted the files inside the /src
dir in the past few days, so my installed zlib and hdf5 dir were also deleted. I think the reason all these errors above is because of that. I have to reinstall all the related libraries : zlib, hdf5. I will do it as fast as I can and hope this time it will work well, if not, I may again ask some questions. Thank you very much Ward for all these helps.
from netcdf-c.
Just some updates on the compilation of netcdf.
I have reinstalled all the related files(zlib, hdf5), successfully installed both of them. But, still could not pass the 'make check' process of netcdf-c, and I also used ifort and icx for the compiler this time.
So next I decided to change the compiler to gcc and gfortran. And finally, successfully installed netcdf.
Again, thanks so much for all the helps.
from netcdf-c.
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from netcdf-c.