LDT Compilation Fails with undefined reference relevant to hdf4 Library

[jinwoongyoo]

I found a LISF post on Discussions with a similar issue, LDT compile issues #1443 but its solution didn't work for me.

When compiling NASA LIS LDT on Discover, LDT compilation fails with undefined reference seemingly relevant to hdf4 library.
Below is what I got in make.log:

ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(putget.o): in function sd_xdr_NCvshort': putget.c:(.text+0x2c): undefined reference to xdr_opaque'
ld: putget.c:(.text+0x58): undefined reference to xdr_opaque' ld: putget.c:(.text+0x112): undefined reference to xdr_opaque'
ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(putget.o): in function xdr_NCv1data': putget.c:(.text+0x6ce): undefined reference to xdr_double'
ld: putget.c:(.text+0x6e7): undefined reference to xdr_float' ld: putget.c:(.text+0x700): undefined reference to xdr_int'
ld: putget.c:(.text+0x743): undefined reference to xdr_opaque' ld: putget.c:(.text+0x7ea): undefined reference to xdr_opaque'
ld: putget.c:(.text+0x844): undefined reference to xdr_opaque' ld: putget.c:(.text+0x886): undefined reference to xdr_opaque'
ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(putget.o): in function xdr_NCvdata': putget.c:(.text+0x3a06): undefined reference to xdr_double'
ld: putget.c:(.text+0x3a14): undefined reference to xdr_float' ld: putget.c:(.text+0x3a22): undefined reference to xdr_int'
ld: putget.c:(.text+0x3a91): undefined reference to xdr_opaque' ld: putget.c:(.text+0x3b2a): undefined reference to xdr_opaque'
ld: putget.c:(.text+0x3ba3): undefined reference to xdr_opaque' ld: putget.c:(.text+0x3c31): undefined reference to xdr_opaque'
ld: putget.c:(.text+0x3cc1): undefined reference to xdr_opaque' ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(putget.o):putget.c:(.text+0x3d5f): more undefined references to xdr_opaque' follow
ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(string.o): in function sd_xdr_NC_string': string.c:(.text+0x278): undefined reference to xdr_u_long'
ld: string.c:(.text+0x31b): undefined reference to xdr_opaque' ld: string.c:(.text+0x391): undefined reference to xdr_u_long'
ld: string.c:(.text+0x3a6): undefined reference to xdr_opaque' ld: string.c:(.text+0x445): undefined reference to xdr_u_long'
ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(var.o): in function sd_xdr_NC_var': var.c:(.text+0x1250): undefined reference to xdr_enum'
ld: var.c:(.text+0x1267): undefined reference to xdr_u_long' ld: var.c:(.text+0x12a7): undefined reference to xdr_u_long'
ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(array.o): in function sd_xdr_NC_array': array.c:(.text+0x1070): undefined reference to xdr_enum'
ld: array.c:(.text+0x1083): undefined reference to xdr_u_long' ld: array.c:(.text+0x15b4): undefined reference to xdr_double'
ld: array.c:(.text+0x15bb): undefined reference to xdr_float' ld: array.c:(.text+0x15c2): undefined reference to xdr_int'
ld: array.c:(.text+0x1619): undefined reference to xdr_opaque' ld: array.c:(.text+0x1643): undefined reference to xdr_opaque'
ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(cdf.o): in function sd_NC_new_cdf': cdf.c:(.text+0xa63): undefined reference to xdr_u_long'
ld: cdf.c:(.text+0xb54): undefined reference to xdr_u_long' ld: cdf.c:(.text+0xb85): undefined reference to xdr_u_long'
ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(cdf.o): in function sd_NC_dup_cdf': cdf.c:(.text+0x4178): undefined reference to xdr_u_long'
ld: cdf.c:(.text+0x424b): undefined reference to xdr_u_long' ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(cdf.o):cdf.c:(.text+0x427c): more undefined references to xdr_u_long' follow
ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(cdf.o): in function xdr_4bytes': cdf.c:(.text+0x66d6): undefined reference to xdr_opaque'
ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(cdf.o): in function sd_xdr_NC_fill': cdf.c:(.text+0x67d2): undefined reference to xdr_double'
ld: cdf.c:(.text+0x67de): undefined reference to xdr_float' ld: cdf.c:(.text+0x67ea): undefined reference to xdr_int'
ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(dim.o): in function sd_xdr_NC_dim': dim.c:(.text+0x8fb): undefined reference to xdr_long'
ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(iarray.o): in function sd_xdr_NC_iarray': iarray.c:(.text+0x174): undefined reference to xdr_u_long'
ld: iarray.c:(.text+0x1f2): undefined reference to xdr_int' ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(putget.o): in function sd_xdr_NCvshort':
putget.c:(.text+0x2c): undefined reference to xdr_opaque' ld: putget.c:(.text+0x58): undefined reference to xdr_opaque'
ld: putget.c:(.text+0x112): undefined reference to xdr_opaque' ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(putget.o): in function xdr_NCv1data':
putget.c:(.text+0x6ce): undefined reference to xdr_double' ld: putget.c:(.text+0x6e7): undefined reference to xdr_float'
ld: putget.c:(.text+0x700): undefined reference to xdr_int' ld: putget.c:(.text+0x743): undefined reference to xdr_opaque'
ld: putget.c:(.text+0x7ea): undefined reference to xdr_opaque' ld: putget.c:(.text+0x844): undefined reference to xdr_opaque'
ld: putget.c:(.text+0x886): undefined reference to xdr_opaque' ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(putget.o): in function xdr_NCvdata':
putget.c:(.text+0x3a06): undefined reference to xdr_double' ld: putget.c:(.text+0x3a14): undefined reference to xdr_float'
ld: putget.c:(.text+0x3a22): undefined reference to xdr_int' ld: putget.c:(.text+0x3a91): undefined reference to xdr_opaque'
ld: putget.c:(.text+0x3b2a): undefined reference to xdr_opaque' ld: putget.c:(.text+0x3ba3): undefined reference to xdr_opaque'
ld: putget.c:(.text+0x3c31): undefined reference to xdr_opaque' ld: putget.c:(.text+0x3cc1): undefined reference to xdr_opaque'
ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(putget.o):putget.c:(.text+0x3d5f): more undefined references to xdr_opaque' follow ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(string.o): in function sd_xdr_NC_string':
string.c:(.text+0x278): undefined reference to xdr_u_long' ld: string.c:(.text+0x31b): undefined reference to xdr_opaque'
ld: string.c:(.text+0x391): undefined reference to xdr_u_long' ld: string.c:(.text+0x3a6): undefined reference to xdr_opaque'
ld: string.c:(.text+0x445): undefined reference to xdr_u_long' ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(var.o): in function sd_xdr_NC_var':
var.c:(.text+0x1250): undefined reference to xdr_enum' ld: var.c:(.text+0x1267): undefined reference to xdr_u_long'
ld: var.c:(.text+0x12a7): undefined reference to xdr_u_long' ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(array.o): in function sd_xdr_NC_array':
array.c:(.text+0x1070): undefined reference to xdr_enum' ld: array.c:(.text+0x1083): undefined reference to xdr_u_long'
ld: array.c:(.text+0x15b4): undefined reference to xdr_double' ld: array.c:(.text+0x15bb): undefined reference to xdr_float'
ld: array.c:(.text+0x15c2): undefined reference to xdr_int' ld: array.c:(.text+0x1619): undefined reference to xdr_opaque'
ld: array.c:(.text+0x1643): undefined reference to xdr_opaque' ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(cdf.o): in function sd_NC_new_cdf':
cdf.c:(.text+0xa63): undefined reference to xdr_u_long' ld: cdf.c:(.text+0xb54): undefined reference to xdr_u_long'
ld: cdf.c:(.text+0xb85): undefined reference to xdr_u_long' ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(cdf.o): in function sd_NC_dup_cdf':
cdf.c:(.text+0x4178): undefined reference to xdr_u_long' ld: cdf.c:(.text+0x424b): undefined reference to xdr_u_long'
ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(cdf.o):cdf.c:(.text+0x427c): more undefined references to xdr_u_long' follow ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(cdf.o): in function xdr_4bytes':
cdf.c:(.text+0x66d6): undefined reference to xdr_opaque' ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(cdf.o): in function sd_xdr_NC_fill':
cdf.c:(.text+0x67d2): undefined reference to xdr_double' ld: cdf.c:(.text+0x67de): undefined reference to xdr_float'
ld: cdf.c:(.text+0x67ea): undefined reference to xdr_int' ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(dim.o): in function sd_xdr_NC_dim':
dim.c:(.text+0x8fb): undefined reference to xdr_long' ld: /discover/nobackup/projects/nu-wrf/lib/ekman/intel-intelmpi/hdf4/lib//libmfhdf.a(iarray.o): in function sd_xdr_NC_iarray':
iarray.c:(.text+0x174): undefined reference to xdr_u_long' ld: iarray.c:(.text+0x1f2): undefined reference to xdr_int'
ld: iarray.c:(.text+0x229): undefined reference to xdr_u_long' ld: iarray.c:(.text+0x255): undefined reference to xdr_int'
make: *** [Makefile:54: LDT] Error 1
[ERR] Compile failed

Any input will be highly appreciated.
Thank you.
Regards,
Jinwoong

[dmocko]

Hi @jinwoongyoo

Are you trying this on Discover Milan nodes? If so, please ensure you are using this environment (and no other modules):

Currently Loaded Modules:
  1) comp/gcc/13.2.0   2) comp/intel/2023.2.1   3) mpi/impi/2021.11   4) git/2.42.0   5) lisf_7.5_intel_2023.2.1

More about using this module on Discover is available in Discussion #1642.

What debug configure level are you using? The above discussion lists known issues with "-3" or "-2".

If the module environment and/or the debug configure level is not the issue, please attach or points us to your configure.ldt file.

[jinwoongyoo]

Hi @dmocko
I was able to compile my LDT successfully.
It turned out that the error was due to my old LIS/LDT version 7.4 that cannot be compiled on the latest lisf_7.5_intel_2023.2.1 library on Discover. Transplanting my modification code into the latest LIS/LDT version 7.5 solved the issue.
Thank you very much!
Regards,
Jinwoong