Cannot install cmor3

[EugeneRozanov]

I am not an experienced user, so I just followed the instructions. Everything went ok until "make" phase. The computer complains about the absence of several mathematical functions (e.g., atan, log10, and so on) in the one of c-written code. The community advised to add -lm flag at the link phase, but I cannot understand where exactly it should be done. Any advice on how to change Makefile or something else?

E. Rozanov

[mauzey1]

@EugeneRozanov Which platform are you building CMOR on? Mac or Linux?

Have you tried rerunning the configure step and then running make install again?

[EugeneRozanov]

I have LINUX, TCSH shell. I repeateted the procedure 4 times and the result was always the same. I have also tried to compile my FORTRAN code. The compilation is OK but the program behave very strange and unpredictable. It looks like all cmor functions are corrupted.

I am very glad somebody answer.

E.

Sent from my Huawei phone

-------- Original message -------- From: mauzey1 notifications@github.com Date: Tue, 19 Jan 2021, 20:53 To: PCMDI/cmor3_documentation cmor3_documentation@noreply.github.com Cc: Eugene Rozanov Eugene.Rozanov@pmodwrc.ch, Mention mention@noreply.github.com Subject: Re: [PCMDI/cmor3_documentation] Cannot install cmor3 (#99)

@EugeneRozanovhttps://github.com/EugeneRozanov Which platform are you building CMOR on? Mac or Linux?

Have you tried rerunning the configure step and then running make install again?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/PCMDI/cmor3_documentation/issues/99#issuecomment-763089310, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ASQV2JIQSLK7RKBQXKK26QTS2XPM5ANCNFSM4WJIYJJA.

[EugeneRozanov]

I moved to another computer and error with “ATAN” did not appear. All test (make test_python) are ok, but test with fortran (make test_fortran) failed with

gfortran: error: unrecognized command line option ‘-fno-plt’

I could not find such option for gfortran and I do not now can it be substituted by something else.

Please, advise.

Eugene

I have LINUX, TCSH shell. I repeateted the procedure 4 times and the result was always the same. I have also tried to compile my FORTRAN code. The compilation is OK but the program behave very strange and unpredictable. It looks like all cmor functions are corrupted.

I am very glad somebody answer.

E.

Sent from my Huawei phone

-------- Original message -------- From: mauzey1 notifications@github.com Date: Tue, 19 Jan 2021, 20:53 To: PCMDI/cmor3_documentation cmor3_documentation@noreply.github.com Cc: Eugene Rozanov Eugene.Rozanov@pmodwrc.ch, Mention mention@noreply.github.com Subject: Re: [PCMDI/cmor3_documentation] Cannot install cmor3 (#99)

@EugeneRozanovhttps://github.com/EugeneRozanov Which platform are you building CMOR on? Mac or Linux?

Have you tried rerunning the configure step and then running make install again?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/PCMDI/cmor3_documentation/issues/99#issuecomment-763089310, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ASQV2JIQSLK7RKBQXKK26QTS2XPM5ANCNFSM4WJIYJJA.

[mauzey1]

@EugeneRozanov It might help if you post the output of conda list for your conda environment as well as the output for make test_fortran.

[EugeneRozanov]

Here they are. How to add

From: mauzey1 notifications@github.com Sent: Wednesday, January 20, 2021 9:06 PM To: PCMDI/cmor3_documentation cmor3_documentation@noreply.github.com Cc: Eugene Rozanov Eugene.Rozanov@pmodwrc.ch; Mention mention@noreply.github.com Subject: Re: [PCMDI/cmor3_documentation] Cannot install cmor3 (#99)

@EugeneRozanovhttps://github.com/EugeneRozanov It might help if you post the output of conda list for your conda environment as well as the output for make test_fortran.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/PCMDI/cmor3_documentation/issues/99#issuecomment-763900040, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ASQV2JOFU5YKJ2LFP7SFZGLS24ZUFANCNFSM4WJIYJJA.

packages in environment at /cluster/work/climate/erozanov/miniconda3/envs/cmor_dev:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge attrs 20.3.0 pyhd3deb0d_0 conda-forge binutils_impl_linux-64 2.35.1 h193b22a_1 conda-forge binutils_linux-64 2.35 hc3fd857_29 conda-forge blas 1.1 openblas conda-forge bokeh 2.2.3 py38h578d9bd_0 conda-forge brotlipy 0.7.0 py38h497a2fe_1001 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.17.1 h36c2ea0_0 conda-forge ca-certificates 2020.12.5 ha878542_0 conda-forge cdat_info 8.2.2020.08.27.15.53.ga42e5c8 pyh9f0ad1d_0 cdat/label/nightly cdms2 3.1.5.2020.11.03.21.54.gf997653 py38h11a58eb_0 cdat/label/nightly cdp 1.7.0 pyhd8ed1ab_0 conda-forge cdtime 3.1.4.2020.10.12.15.52.g2b715b5 py38hac60b08_0 cdat/label/nightly certifi 2020.12.5 py38h578d9bd_1 conda-forge cffi 1.14.4 py38ha65f79e_1 conda-forge cftime 1.3.1 py38h5c078b8_0 conda-forge chardet 4.0.0 py38h578d9bd_1 conda-forge click 7.1.2 pyh9f0ad1d_0 conda-forge cloudpickle 1.6.0 py_0 conda-forge cmor 3.6.1 pypi_0 pypi cryptography 3.3.1 py38h2b97feb_1 conda-forge curl 7.71.1 he644dc0_8 conda-forge cytoolz 0.11.0 py38h25fe258_1 conda-forge dask 2021.1.0 pyhd8ed1ab_0 conda-forge dask-core 2021.1.0 pyhd8ed1ab_0 conda-forge distarray 2.12.2 py_1 conda-forge distributed 2021.1.0 py38h578d9bd_1 conda-forge esmf 8.0.1 nompi_hcaa3220_2 conda-forge esmpy 8.0.1 nompi_py38h5410a82_2 conda-forge expat 2.2.9 he1b5a44_2 conda-forge flake8 3.8.4 py_0 conda-forge freetype 2.10.4 h0708190_1 conda-forge fsspec 0.8.5 pyhd8ed1ab_0 conda-forge future 0.18.2 py38h578d9bd_3 conda-forge g2clib 1.6.0 hf3f1b0b_9 conda-forge gcc_impl_linux-64 7.5.0 hda68d29_13 conda-forge gcc_linux-64 7.5.0 he2a3fca_29 conda-forge gfortran_impl_linux-64 7.5.0 h56cb351_18 conda-forge gfortran_linux-64 7.5.0 ha081f1e_29 conda-forge hdf4 4.2.13 h10796ff_1004 conda-forge hdf5 1.10.6 nompi_h7c3c948_1111 conda-forge heapdict 1.0.1 py_0 conda-forge idna 2.10 pyh9f0ad1d_0 conda-forge importlib-metadata 3.4.0 py38h578d9bd_0 conda-forge importlib_metadata 3.4.0 hd8ed1ab_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge jasper 1.900.1 h07fcdf6_1006 conda-forge jinja2 2.11.2 pyh9f0ad1d_0 conda-forge jpeg 9d h36c2ea0_0 conda-forge json-c 0.13.1 hbfbb72e_1002 conda-forge jsonschema 3.2.0 py_2 conda-forge jupyter_core 4.7.0 py38h578d9bd_0 conda-forge kernel-headers_linux-64 2.6.32 h77966d4_13 conda-forge krb5 1.17.2 h926e7f8_0 conda-forge lazy-object-proxy 1.5.2 py38h497a2fe_1 conda-forge lcms2 2.11 hcbb858e_1 conda-forge ld_impl_linux-64 2.35.1 hea4e1c9_1 conda-forge libblas 3.8.0 17_openblas conda-forge libcblas 3.8.0 17_openblas conda-forge libcdms 3.1.2 h054cd8a_113 conda-forge libcf 1.0.3 py38h88b7cc0_109 conda-forge libcurl 7.71.1 hcdd3856_8 conda-forge libdrs 3.1.2 hc2e2db3_113 conda-forge libdrs_f 3.1.2 hae7e664_111 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libffi 3.3 h58526e2_2 conda-forge libgcc-ng 9.3.0 h2828fa1_18 conda-forge libgfortran-ng 7.5.0 h14aa051_18 conda-forge libgfortran4 7.5.0 h14aa051_18 conda-forge libgomp 9.3.0 h2828fa1_18 conda-forge libnetcdf 4.7.4 nompi_h56d31a8_107 conda-forge libnghttp2 1.41.0 h8cfc5f6_2 conda-forge libopenblas 0.3.10 h5a2b251_0
libpng 1.6.37 h21135ba_2 conda-forge libssh2 1.9.0 hab1572f_5 conda-forge libstdcxx-ng 9.3.0 h6de172a_18 conda-forge libtiff 4.2.0 hdc55705_0 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libwebp-base 1.1.0 h36c2ea0_3 conda-forge locket 0.2.0 py_2 conda-forge lz4-c 1.9.3 h9c3ff4c_0 conda-forge markupsafe 1.1.1 py38h497a2fe_3 conda-forge mccabe 0.6.1 py_1 conda-forge msgpack-python 1.0.2 py38h1fd1430_1 conda-forge nbformat 5.1.2 pyhd8ed1ab_1 conda-forge ncurses 6.2 h58526e2_4 conda-forge netcdf-fortran 4.5.3 nompi_hfef6a68_101 conda-forge netcdf4 1.5.5.1 nompi_py38h1cdf482_100 conda-forge nose 1.3.7 py_1006 conda-forge numpy 1.19.2 py38h6163131_0
numpy-base 1.19.2 py38h75fe3a5_0
olefile 0.46 pyh9f0ad1d_1 conda-forge openblas 0.3.3 h9ac9557_1001 conda-forge openssl 1.1.1i h7f98852_0 conda-forge output_viewer 1.3.1 py_1 conda-forge packaging 20.8 pyhd3deb0d_0 conda-forge pandas 1.2.0 py38h51da96c_1 conda-forge partd 1.1.0 py_0 conda-forge pillow 8.1.0 py38h357d4e7_1 conda-forge pip 20.3.3 pyhd8ed1ab_0 conda-forge psutil 5.8.0 py38h497a2fe_1 conda-forge pycodestyle 2.6.0 pyh9f0ad1d_0 conda-forge pycparser 2.20 pyh9f0ad1d_2 conda-forge pyflakes 2.2.0 pyh9f0ad1d_0 conda-forge pyopenssl 20.0.1 pyhd8ed1ab_0 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pyrsistent 0.17.3 py38h497a2fe_2 conda-forge pysocks 1.7.1 py38h578d9bd_3 conda-forge python 3.8.6 hffdb5ce_4_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python_abi 3.8 1_cp38 conda-forge pytz 2020.5 pyhd8ed1ab_0 conda-forge pyyaml 5.3.1 py38h497a2fe_2 conda-forge readline 8.0 he28a2e2_2 conda-forge requests 2.25.1 pyhd3deb0d_0 conda-forge setuptools 49.6.0 py38h578d9bd_3 conda-forge six 1.15.0 pyh9f0ad1d_0 conda-forge sortedcontainers 2.3.0 pyhd8ed1ab_0 conda-forge sqlite 3.34.0 h74cdb3f_0 conda-forge sysroot_linux-64 2.12 h77966d4_13 conda-forge tblib 1.6.0 py_0 conda-forge testsrunner 8.2.2020.07.01.05.42.g3cf5a0b pyh9f0ad1d_0 cdat/label/nightly tk 8.6.10 h21135ba_1 conda-forge toolz 0.11.1 py_0 conda-forge tornado 6.1 py38h497a2fe_1 conda-forge traitlets 5.0.5 py_0 conda-forge typing_extensions 3.7.4.3 py_0 conda-forge udunits2 2.2.27.27 h360fe7b_0 conda-forge urllib3 1.26.2 pyhd8ed1ab_0 conda-forge wheel 0.36.2 pyhd3deb0d_0 conda-forge xz 5.2.5 h516909a_1 conda-forge yaml 0.2.5 h516909a_0 conda-forge zict 2.0.0 py_0 conda-forge zipp 3.4.0 py_0 conda-forge zlib 1.2.11 h516909a_1010 conda-forge zstd 1.4.8 ha95c52a_1 conda-forge

[mauzey1]

@EugeneRozanov I'm still not sure what is going wrong with your build. The gfortran compiler not recognizing the option -fno-plt might indicate that an older version of gcc is being used. Check your Makefile's FC and CC variables to see where the compilers are coming from. Does running make test_C work?

[EugeneRozanov]

Thanks. I checked and corrected gcc. It works now. E.

From: mauzey1 notifications@github.com Sent: Tuesday, January 26, 2021 3:32 AM To: PCMDI/cmor3_documentation cmor3_documentation@noreply.github.com Cc: Eugene Rozanov Eugene.Rozanov@pmodwrc.ch; Mention mention@noreply.github.com Subject: Re: [PCMDI/cmor3_documentation] Cannot install cmor3 (#99)

@EugeneRozanovhttps://github.com/EugeneRozanov I'm still not sure what is going wrong with your build. The gfortran compiler not recognizing the option -fno-plt might indicate that an older version of gcc is being used. Check your Makefile's FC and CC variables to see where the compilers are coming from. Does running make test_C work?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/PCMDI/cmor3_documentation/issues/99#issuecomment-767246607, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ASQV2JLINTGMORNMKRWG5Q3S3YSTDANCNFSM4WJIYJJA.