libmesh Installation on centOS 7.9: undefined ref to strlcat

[ischeider]

Hi everybody,
I struggle installing libmesh for the moose framework. The configure runs smoothly, but make tells me undefined reference to strlcat at several places. You'll find the config.log attached.
config.log

There is also some output

...
checking for execinfo.h... yes
checking for strlcat... yes
checking for snprintf... yes
...

The important part of the make output is

make[4]: Entering directory `/gpfs/home/scheider/software/libmesh/build/contrib/netcdf/netcdf-c/libnczarr'
  CC       libnczarr_la-zarr.lo
  CC       libnczarr_la-zattr.lo
  CC       libnczarr_la-zxcache.lo
  CC       libnczarr_la-zchunking.lo
  CC       libnczarr_la-zclose.lo
  CC       libnczarr_la-zcreate.lo
  CC       libnczarr_la-zcvt.lo
  CC       libnczarr_la-zdim.lo
  CC       libnczarr_la-zfile.lo
  CC       libnczarr_la-zdispatch.lo
  CC       libnczarr_la-zgrp.lo
  CC       libnczarr_la-zinternal.lo
../../../../../contrib/netcdf/netcdf-c/libnczarr/zxcache.c: In function 'NCZ_printxcache':
../../../../../contrib/netcdf/netcdf-c/libnczarr/zxcache.c:888:5: warning: implicit declaration of function 'strlcat'; did you mean 'strncat'? [-Wimplicit-function-declaration]
  888 |     strlcat(xs,ncbytescontents(buf),sizeof(xs));
      |     ^~~~~~~
      |     strncat
  CC       libnczarr_la-zmap.lo
  CC       libnczarr_la-zmap_file.lo
  CC       libnczarr_la-zodom.lo
  CC       libnczarr_la-zopen.lo
  CC       libnczarr_la-zprov.lo
  CC       libnczarr_la-zsync.lo
  CC       libnczarr_la-ztype.lo
  CC       libnczarr_la-zutil.lo
  CC       libnczarr_la-zvar.lo
  CC       libnczarr_la-zwalk.lo
  CC       libnczarr_la-zdebug.lo
../../../../../contrib/netcdf/netcdf-c/libnczarr/zmap_file.c: In function 'zffullpath':
../../../../../contrib/netcdf/netcdf-c/libnczarr/zmap_file.c:615:5: warning: implicit declaration of function 'strlcat'; did you mean 'strncat'? [-Wimplicit-function-declaration]
  615 |     strlcat(path,zfmap->root,flen);
      |     ^~~~~~~
      |     strncat
  CC       libnczarr_la-zfilter.lo
../../../../../contrib/netcdf/netcdf-c/libnczarr/zutil.c: In function 'NCZ_chunkpath':
../../../../../contrib/netcdf/netcdf-c/libnczarr/zutil.c:940:5: warning: implicit declaration of function 'strlcat'; did you mean 'strncat'? [-Wimplicit-function-declaration]
  940 |     strlcat(path,key.varkey,plen+1);
      |     ^~~~~~~
      |     strncat
../../../../../contrib/netcdf/netcdf-c/libnczarr/zfilter.c: In function 'NCZ_load_plugin_dir':
../../../../../contrib/netcdf/netcdf-c/libnczarr/zfilter.c:1354:9: warning: implicit declaration of function 'strlcat'; did you mean 'strncat'? [-Wimplicit-function-declaration]
 1354 |         strlcat(file,path,flen);
      |         ^~~~~~~
      |         strncat
  CCLD     libnczarr.la
make[4]: Leaving directory `/gpfs/home/scheider/software/libmesh/build/contrib/netcdf/netcdf-c/libnczarr'
Making all in liblib
make[4]: Entering directory `/gpfs/home/scheider/software/libmesh/build/contrib/netcdf/netcdf-c/liblib'
  CC       libnetcdf_la-nc_initialize.lo
  CCLD     libnetcdf.la
libtool: warning: '/project/opt/gcc_132/lib64/libgfortran.la' seems to be moved
libtool: warning: '/project/opt/gcc_132/lib64/libquadmath.la' seems to be moved
libtool: warning: '/project/opt/gcc_132/lib64/libstdc++.la' seems to be moved
/usr/bin/ld: cannot find /gpfs/home/scheider/software/libmesh/build/contrib/netcdf/netcdf-c/liblib/.libs/libnetcdf.so: No such file or directory
collect2: error: ld returned 1 exit status
make[4]: *** [libnetcdf.la] Error 1

The only hint I found on the internet ist to use LDFLAGS=-lbsd which I did - no improvements.
Is there anybody out there who can tell me what I missed/overlooked?
Thanks in advance

[jwpeterson]

If I understand correctly, strlcat is a non-standard BSD function, so I'm a bit surprised that configure detects it on your centOS system. I don't have that function on my Ubuntu system, but if you do, apparently it should be defined in <string.h>. So one thing you could try is including <string.h> from the file zxcache.c that complains about the implicit declaration, although I doubt that will really fix anything.

The messages you pasted above are just warnings about implicit declarations... the actual error seems to be a linking error:

/usr/bin/ld: cannot find /gpfs/home/scheider/software/libmesh/build/contrib/netcdf/netcdf-c/liblib/.libs/libnetcdf.so: No such file or directory
collect2: error: ld returned 1 exit status

but it's not clear what the actual linking error is. It might be related to strlcat, or it might be something else entirely...

[ischeider]

Thank you for the quick response, and sorry, the reason why the error in the above output is somewhere else is that I ran it again (and some parts were left out apparently), so I posted the wrong output. After a make distclean and rerunning everything I could reproduce the error, which indeed in an undefined reference to strlcat:

Making all in ncgen3
make[4]: Entering directory `/gpfs/home/scheider/software/libmesh/build/contrib/netcdf/netcdf-c/ncgen3'
  CC       main.o
  CC       load.o
../../../../../contrib/netcdf/netcdf-c/ncgen3/load.c: In function ‘gen_load_c’:
../../../../../contrib/netcdf/netcdf-c/ncgen3/load.c:104:13: warning: implicit declaration of function ‘strlcat’; did you mean ‘strncat’? [-Wimplicit-function-declaration]
  104 |             strlcat(stmnt, s2, C_MAX_STMNT);
      |             ^~~~~~~
      |             strncat
  CC       escapes.o
  CC       getfill.o
  CC       init.o
  CC       genlib.o
../../../../../contrib/netcdf/netcdf-c/ncgen3/genlib.c: In function ‘decodify’:
../../../../../contrib/netcdf/netcdf-c/ncgen3/genlib.c:1970:15: warning: implicit declaration of function ‘strlcat’; did you mean ‘strncat’? [-Wimplicit-function-declaration]
 1970 |         len = strlcat(sp, repls[j], newlen);
      |               ^~~~~~~
      |               strncat
  CC       ncgeny.o
  CCLD     ncgen3
load.o: In function `gen_load_c':
load.c:(.text+0x391): undefined reference to `strlcat'
load.c:(.text+0xec2): undefined reference to `strlcat'
load.c:(.text+0xee0): undefined reference to `strlcat'
load.o: In function `fstrcat':
load.c:(.text+0x1053): undefined reference to `strlcat'
genlib.o: In function `decodify':
genlib.c:(.text+0x51e7): undefined reference to `strlcat'
collect2: error: ld returned 1 exit status
make[4]: *** [ncgen3] Error 1

I also see that all some of the functions complaining about implicit declaration have <string.h> in their header.
BTW: On my ubuntu system I also don't have any problem with the installation (even though it says checking for strlcat... yes there, too).

[roystgnr]

This seems potentially relevant to me:

libtool: warning: '/project/opt/gcc_132/lib64/libstdc++.la' seems to be moved

/usr/bin/ld: cannot find

You've got a custom libstdc++, but netcdf is trying to use the system linker? strlcat is supposed to be defined in libc.so, but it could be that you're getting one libc's headers at compile time but a different libc at link time. I'd nm -D /both/options/libc.so.whatever | grep strlcat and see if that's a possibility.

[ischeider]

Thanks for your suggestion!

I checked all libraries in my gcc_132 installation as well as the ones in /lib64, none of them (except some special ones like libkde*.so and libruby.so) contains strlcat. But I found the function in my netcdf4.9.2 installation. Thus I tried without my netcdf and hdf5, using --netcdf=v492, but without enable-hdf5. Result: IT WORKS!. However, when I load the hdf5 module (but not netcdf, so that no netcdf stuff is in any of the environment variables) and --enable-hdf5, it again shows the same error, even though there is not strlcat in the hdf5 libraries. (hdf5 does not seem to be a requirement for moose, so it will probably work without).

[roystgnr]

HDF5 isn't a requirement for MOOSE, but it is an extended capability. If you build without it the most important thing you'll lose is the ability to read ExodusII files that were written on top of HDF5. By default MOOSE writes even ExodusII files without HDF5 (I think it defaults to NetCDF3 format?) but you may lose compatibility with some third-party files.