Compilation of RTTOV-14 using conda

[Sylvain Heilliette]

Hi All,

I tried to use the recipe described in point 9) of RTTOV FAQ (https://nwp-saf.eumetsat.int/site/software/rttov/documentation/rttov-faqs/)

The compilation started well. But if failed at the link stage:

cd ../../tmp-gfortran-conda/test && /home/syh074/.conda/envs/rttov14/bin/gfortran -I../../forPython/include -D_RTTOV_NETCDF -I/home/syh074/.conda/envs/rttov14//include -fPIC -O3 -ffree-line-length-none -fmax-stack-var-size=128000 -I../../forPython/mod -c ../../src/test/example_aer_file_fwd.F90 -o ../../forPython/obj/example_aer_file_fwd.o
cd ../../tmp-gfortran-conda/test && /home/syh074/.conda/envs/rttov14/bin/gfortran -o ../../forPython/bin/example_aer_file_fwd.exe ../../forPython/obj/example_aer_file_fwd.o -L../../forPython/lib -lrttov14_test -lrttov14_brdf_atlas -lrttov14_other -lrttov14_emis_atlas -lrttov14_coef_io -lrttov14_netcdf -lrttov14_parallel -lrttov14_main -L/home/syh074/.conda/envs/rttov14//lib -lnetcdff -lnetcdf -lnetcdf -lhdf5_hl -lhdf5 -lsz -lz -lcurl -lm
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libdl.so.2: undefined reference to `_dl_catch_error@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libpthread.so.0: undefined reference to `__nanosleep_nocancel@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libdl.so.2: undefined reference to `_dl_signal_error@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libpthread.so.0: undefined reference to `__twalk@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libpthread.so.0: undefined reference to `__call_tls_dtors@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libpthread.so.0: undefined reference to `__tsearch@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libpthread.so.0: undefined reference to `__mmap@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libpthread.so.0: undefined reference to `__tdelete@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libpthread.so.0: undefined reference to `_IO_enable_locks@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libpthread.so.0: undefined reference to `__tfind@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libpthread.so.0: undefined reference to `__sigtimedwait@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libpthread.so.0: undefined reference to `__libc_fcntl64@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libpthread.so.0: undefined reference to `__pause_nocancel@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libpthread.so.0: undefined reference to `__tunable_get_val@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libpthread.so.0: undefined reference to `__write_nocancel@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libpthread.so.0: undefined reference to `__mprotect@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libpthread.so.0: undefined reference to `__munmap@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libpthread.so.0: undefined reference to `__open64_nocancel@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libpthread.so.0: undefined reference to `__read_nocancel@GLIBC_PRIVATE’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /lib64/libpthread.so.0: undefined reference to `__close_nocancel@GLIBC_PRIVATE’
collect2: error: ld returned 1 exit status

It is possible to I put wrong information in my gfortran-conda arch file.
In particular I was not sure on how to interpret step 5:

5. Update LDFLAGS: LDFLAGS=”-shared $LDFLAGS”

Here is my gfortran-conda arch file:

FC=/home/syh074/.conda/envs/rttov14/bin/gfortran
FC77=/home/syh074/.conda/envs/rttov14/bin/gfortran
CC=/home/syh074/.conda/envs/rttov14/bin/gcc
LDFLAGS_ARCH=
CFLAGS_ARCH= -std=c89
FFLAGS_ARCH=-fPIC -O3 -ffree-line-length-none -fmax-stack-var-size=128000
AR=ar r
#LDFLAGS=”-shared $LDFLAGS”
F2PY=f2py –fcompiler=gnu95
F2PYFLAGS_ARCH=”-fPIC -ffree-line-length-none”
F2PYLDFLAGS_ARCH=
FFLAGS_ARCH_lapack=-fPIC -O3

Any suggestion ?

Many Thanks,

Sylvain Heilliette

[James Hocking]

Hi Sylvain,

Can you try adding -shared to LDFLAGS_ARCH? I could replicate the error you got without this, and adding it fixed the issue.

You may need to install meson in your conda environment too.

I have updated the FAQ to reflect the above.

Best wishes,
James

[Sylvain Heilliette]

Many thanks for your suggestion.

With your modification, I now get another error message:

cd ../../tmp-gfortran-conda/mw_scatt_coef && /home/syh074/.conda/envs/rttov14/bin/gfortran -o ../../test/bin/rttov_scatt_make_coef.exe ../../test/obj/rttov_scatt_make_coef.o -L../../test/lib -lrttov14_mw_scatt_coef -lrttov14_other -lrttov14_coef_io -lrttov14_netcdf -lrttov14_main -L/home/syh074/.conda/envs/rttov14//lib -lnetcdff -lnetcdf -lnetcdf -lhdf5_hl -lhdf5 -lsz -lz -lcurl -lm -shared
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../test/lib/librttov14_mw_scatt_coef.a(scatdb.o): warning: relocation against stderr@@GLIBC_2.2.5' in read-only section.text’
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../test/lib/librttov14_mw_scatt_coef.a(scatdb.o): relocation R_X86_64_PC32 against symbol `stderr@@GLIBC_2.2.5′ can not be used when making a shared object; recompile with -fPIC
/fs/site5/eccc/mrd/rpndat/syh074/.conda/envs/rttov14/bin/../lib/gcc/x86_64-conda-linux-gnu/15.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:84: ../../test/bin/rttov_scatt_make_coef.exe] Error 1
make[1]: Leaving directory ‘/fs/homeu2/eccc/mrd/rpndat/syh074/codedir/rttov14OfficielGfortran/src/mw_scatt_coef’
make: *** [Makefile:27: mw_scatt_coef/bin] Error 2

I will look into meson to if it might help.

[James Hocking]

Hi Sylvain,

Apologies, I forgot that I also had to add -fPIC to CFLAGS_ARCH (I got the same error). This seems to be something new with the latest version of gcc (v15).

Regarding meson, you need this if you are building the Python wrapper and you are using Numpy v2.x.

Best wishes,
James

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