[ncl-install] Fwd: installation tests work but ncargf90 does not run
Orhan Eroglu
oero at ucar.edu
Thu Aug 12 10:07:08 MDT 2021
Hi Simon,
Thanks for letting me know your updates! I am glad you got what you needed,
and I am sorry I could not help further.
Just FYI: Since people who are willing to use conda are still vulnerable to
the existing issue, I am still planning to dig into the conda-related
issue, and will still keep you posted if I can find a solution.
Best,
On Wed, Aug 11, 2021 at 5:11 PM Simon J Mason <simon at iri.columbia.edu>
wrote:
> Dear Orhan,
>
> I decided to do things the old way and installed by compiling the source
> code. It took a few attempts to make
> sure I had all the relevant software installed and compiler options
> correct, but I do now have ncargf90 working.
>
> For some reason, ctrans -d X11 just gives me a blank image, but I
> typically have NCAR Graphics programs
> generating .ps files, and those look to be working ok, so I have what I
> need working for now.
>
> Many thanks,
>
> Simon
>
>
> On 8/3/2021 11:08 AM, Orhan Eroglu wrote:
>
> Hi Simon,
>
> Although I couldn't fix it fully, I'd like to share my findings with you:
>
> As @Andrei Kurbatov <akurbatov at maine.edu> suggested in a different post,
> this is a compiler issue (Both gfortran and gcc). For example, in your
> platform, I can understand from your outputs that it is trying to
> run gfortran compiler at `
> */home/conda/feedstock_root/build_artifacts/ncl_1602173391809/_build_env/bin/x86_64-conda-linux-gnu-gfortran*`
> and can't find it.
>
> FYI: gfortran and gcc compilers are also not being set properly after my
> NCL installation via conda in my MacOS environment, and I couldn't get it
> fixed yet though I attempted to manually point to compilers' correct
> locations in my system. Therefore, I couldn't fix this issue yet,
> unfortunately. I have been following up with another NCL user on the exact
> same issue, and I will let you know if I can find anything here.
>
> Sorry for any inconveniences.
>
> On Mon, Aug 2, 2021 at 2:50 PM Simon Mason <simon at iri.columbia.edu> wrote:
>
>> I have tried to run some updates, but am still having no success running
>> ncargf90.
>>
>> I get the following error message:
>>
>> /home/conda/feedstock_root/build_artifacts/ncl_1602173391809/_build_env/bin/x86_64-conda-linux-gnu-gfortran
>> -fPIC -fno-second-underscore -fno-range-check -fopenmp -O
>> -L/home/simon/anaconda3/envs/ncl_stable/lib -Wl,-O2 -Wl,--sort-common
>> -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags
>> -Wl,--gc-sections -Wl,-rpath,/home/simon/anaconda3/envs/ncl_stable/lib
>> -Wl,-rpath-link,/home/simon/anaconda3/envs/ncl_stable/lib
>> -L/home/simon/anaconda3/envs/ncl_stable/lib maps.f95
>> -L/home/simon/anaconda3/envs/ncl_stable/lib -L/usr/X11R6/lib64 -lncarg
>> -lncarg_gks -lncarg_c -lX11 -lXext -lcairo -lXrender -lfontconfig
>> -lpixman-1 -lfreetype -lexpat -lpng -lz -lbz2
>> /home/conda/feedstock_root/build_artifacts/ncl_1602173391809/_build_env/bin/x86_64-conda-linux-gnu-gfortran:
>> Command not found.
>>
>> I get the following outputs from the commands listed:
>>
>> > conda --version
>>
>> conda 4.10.3
>>
>> > which ncl
>>
>> /home/simon/anaconda3/envs/ncl_stable/bin/ncl
>>
>> > ncl -V
>>
>> 6.6.2
>>
>> > env | grep NCARG
>>
>> NCARG_ROOT=/home/simon/anaconda3/envs/ncl_stable
>>
>> > conda list -n ncl_stable
>> # packages in environment at /home/simon/anaconda3/envs/ncl_stable:
>> #
>> # Name Version Build Channel
>> _libgcc_mutex 0.1 conda_forge conda-forge
>> _openmp_mutex 4.5 1_gnu conda-forge
>> binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge
>> binutils_linux-64 2.36 hf3e587d_33 conda-forge
>> boost-cpp 1.74.0 h9359b55_0 conda-forge
>> bzip2 1.0.8 h7f98852_4 conda-forge
>> c-ares 1.17.1 h7f98852_1 conda-forge
>> ca-certificates 2021.5.30 ha878542_0 conda-forge
>> cairo 1.16.0 h488836b_1006 conda-forge
>> cfitsio 3.470 h2e3daa1_7 conda-forge
>> curl 7.76.1 h979ede3_1 conda-forge
>> esmf 8.0.1 nompi_hcaa3220_2 conda-forge
>> expat 2.4.1 h9c3ff4c_0 conda-forge
>> fontconfig 2.13.1 hba837de_1005 conda-forge
>> freetype 2.10.4 h0708190_1 conda-forge
>> freexl 1.0.6 h7f98852_0 conda-forge
>> gcc_impl_linux-64 7.5.0 habd7529_19 conda-forge
>> gcc_linux-64 7.5.0 h47867f9_33 conda-forge
>> geos 3.8.1 he1b5a44_0 conda-forge
>> geotiff 1.6.0 h5d11630_3 conda-forge
>> gettext 0.19.8.1 h0b5b191_1005 conda-forge
>> gfortran_impl_linux-64 7.5.0 h56cb351_19 conda-forge
>> gfortran_linux-64 7.5.0 h78c8a43_33 conda-forge
>> giflib 5.2.1 h36c2ea0_2 conda-forge
>> gsl 2.6 he838d99_2 conda-forge
>> hdf4 4.2.15 h10796ff_3 conda-forge
>> hdf5 1.10.6 nompi_h7c3c948_1111
>> conda-forge
>> hdfeos2 2.20 h64bfcee_1000 conda-forge
>> hdfeos5 5.1.16 hb4ce793_7 conda-forge
>> icu 67.1 he1b5a44_0 conda-forge
>> jasper 1.900.1 h07fcdf6_1006 conda-forge
>> jpeg 9d h36c2ea0_0 conda-forge
>> json-c 0.13.1 hbfbb72e_1002 conda-forge
>> kealib 1.4.14 hcc255d8_2 conda-forge
>> kernel-headers_linux-64 2.6.32 he073ed8_14 conda-forge
>> krb5 1.17.2 h926e7f8_0 conda-forge
>> ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
>> libblas 3.9.0 8_openblas conda-forge
>> libcblas 3.9.0 8_openblas conda-forge
>> libcurl 7.76.1 hc4aaa36_1 conda-forge
>> libdap4 3.20.6 hd7c4107_2 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-devel_linux-64 7.5.0 hda03d7c_19 conda-forge
>> libgcc-ng 11.1.0 hc902ee8_6 conda-forge
>> libgdal 3.1.4 h50e41a3_1 conda-forge
>> libgfortran-ng 7.5.0 h14aa051_19 conda-forge
>> libgfortran4 7.5.0 h14aa051_19 conda-forge
>> libglib 2.68.3 h3e27bee_0 conda-forge
>> libgomp 11.1.0 hc902ee8_6 conda-forge
>> libiconv 1.16 h516909a_0 conda-forge
>> libkml 1.3.0 h238a007_1014 conda-forge
>> libnetcdf 4.7.4 nompi_h56d31a8_107
>> conda-forge
>> libnghttp2 1.43.0 h812cca2_0 conda-forge
>> libopenblas 0.3.12 pthreads_hb3c22a3_1
>> conda-forge
>> libpng 1.6.37 h21135ba_2 conda-forge
>> libpq 12.3 h255efa7_3 conda-forge
>> librttopo 1.1.0 hb271727_4 conda-forge
>> libspatialite 5.0.1 h6ec7341_0 conda-forge
>> libssh2 1.9.0 ha56f1ee_6 conda-forge
>> libstdcxx-ng 11.1.0 h56837e0_6 conda-forge
>> libtiff 4.2.0 hbd63e13_2 conda-forge
>> libuuid 2.32.1 h7f98852_1000 conda-forge
>> libwebp-base 1.2.0 h7f98852_2 conda-forge
>> libxcb 1.13 h7f98852_1003 conda-forge
>> libxml2 2.9.10 h68273f3_2 conda-forge
>> lz4-c 1.9.3 h9c3ff4c_1 conda-forge
>> ncl 6.6.2 h087f628_23 conda-forge
>> ncurses 6.2 h58526e2_4 conda-forge
>> netcdf-fortran 4.5.3 nompi_hfef6a68_101
>> conda-forge
>> openjpeg 2.4.0 hb52868f_1 conda-forge
>> openssl 1.1.1k h7f98852_0 conda-forge
>> pcre 8.45 h9c3ff4c_0 conda-forge
>> pixman 0.38.0 h516909a_1003 conda-forge
>> poppler 0.89.0 h2de54a5_5 conda-forge
>> poppler-data 0.4.10 0 conda-forge
>> postgresql 12.3 hc2f5b80_3 conda-forge
>> proj 7.1.1 h966b41f_3 conda-forge
>> pthread-stubs 0.4 h36c2ea0_1001 conda-forge
>> readline 8.1 h46c0cb4_0 conda-forge
>> sqlite 3.36.0 h9cd32fc_0 conda-forge
>> sysroot_linux-64 2.12 he073ed8_14 conda-forge
>> tiledb 2.1.6 h91fcb0e_1 conda-forge
>> tk 8.6.10 h21135ba_1 conda-forge
>> tzcode 2021a h7f98852_2 conda-forge
>> udunits2 2.2.27.27 h975c496_1 conda-forge
>> xerces-c 3.2.3 hfe33f54_1 conda-forge
>> xorg-imake 1.0.7 0 conda-forge
>> xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
>> xorg-libice 1.0.10 h7f98852_0 conda-forge
>> xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
>> xorg-libx11 1.6.12 h36c2ea0_0 conda-forge
>> xorg-libxau 1.0.9 h7f98852_0 conda-forge
>> xorg-libxaw 1.0.14 h7f98852_0 conda-forge
>> xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
>> xorg-libxext 1.3.4 h516909a_0 conda-forge
>> xorg-libxmu 1.1.3 h516909a_0 conda-forge
>> xorg-libxpm 3.5.13 h516909a_0 conda-forge
>> xorg-libxrender 0.9.10 h516909a_1002 conda-forge
>> xorg-libxt 1.1.5 h516909a_1003 conda-forge
>> xorg-makedepend 1.0.6 he1b5a44_1 conda-forge
>> xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
>> xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
>> xorg-xproto 7.0.31 h7f98852_1007 conda-forge
>> xz 5.2.5 h516909a_1 conda-forge
>> zlib 1.2.11 h516909a_1010 conda-forge
>> zstd 1.4.9 ha95c52a_0 conda-forge
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On 7/22/21 9:32 AM, Simon Mason wrote:
>>
>> ... To elaborate, the error messages I receive are:
>>
>> 1. Before conda activate
>>
>> f77 -fPIC -g -O2 -fdebug-prefix-map=/build/ncl-ncarg=.
>> -fstack-protector-strong -fno-second-underscore -fno-range-check -fPIE
>> -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -L../../../.././shared
>> maps.f95 -L/usr/lib/x86_64-linux-gnu/ncarg -lncarg -lncarg_gks -lncarg_c
>> -lX11 -lXext -lcairo -lXrender -lfontconfig -lpixman-1 -lfreetype -lexpat
>> -lpng -lz -lbz2
>> /usr/bin/ld: cannot find -lX11
>> /usr/bin/ld: cannot find -lXext
>> /usr/bin/ld: cannot find -lcairo
>> /usr/bin/ld: cannot find -lXrender
>> /usr/bin/ld: cannot find -lfontconfig
>> /usr/bin/ld: cannot find -lpixman-1
>> /usr/bin/ld: cannot find -lfreetype
>> /usr/bin/ld: cannot find -lexpat
>> /usr/bin/ld: cannot find -lpng
>> /usr/bin/ld: cannot find -lz
>> /usr/bin/ld: cannot find -lbz2
>> collect2: error: ld returned 1 exit status# packages in environment at
>> /home/simon/anaconda3/envs/ncl_stable:
>> #
>> # Name Version Build Channel
>> _libgcc_mutex 0.1 conda_forge conda-forge
>> _openmp_mutex 4.5 1_gnu conda-forge
>> boost-cpp 1.74.0 h9359b55_0 conda-forge
>> bzip2 1.0.8 h7f98852_4 conda-forge
>> c-ares 1.17.1 h7f98852_1 conda-forge
>> ca-certificates 2021.5.30 ha878542_0 conda-forge
>> cairo 1.16.0 h488836b_1006 conda-forge
>> cfitsio 3.470 h2e3daa1_7 conda-forge
>> curl 7.76.1 h979ede3_1 conda-forge
>> esmf 8.0.1 nompi_hcaa3220_2 conda-forge
>> expat 2.4.1 h9c3ff4c_0 conda-forge
>> fontconfig 2.13.1 hba837de_1005 conda-forge
>> freetype 2.10.4 h0708190_1 conda-forge
>> freexl 1.0.6 h7f98852_0 conda-forge
>> geos 3.8.1 he1b5a44_0 conda-forge
>> geotiff 1.6.0 h5d11630_3 conda-forge
>> gettext 0.19.8.1 h0b5b191_1005 conda-forge
>> giflib 5.2.1 h36c2ea0_2 conda-forge
>> gsl 2.6 he838d99_2 conda-forge
>> hdf4 4.2.15 h10796ff_3 conda-forge
>> hdf5 1.10.6 nompi_h7c3c948_1111
>> conda-forge
>> hdfeos2 2.20 h64bfcee_1000 conda-forge
>> hdfeos5 5.1.16 hb4ce793_7 conda-forge
>> icu 67.1 he1b5a44_0 conda-forge
>> jasper 1.900.1 h07fcdf6_1006 conda-forge
>> jpeg 9d h36c2ea0_0 conda-forge
>> json-c 0.13.1 hbfbb72e_1002 conda-forge
>> kealib 1.4.14 hcc255d8_2 conda-forge
>> krb5 1.17.2 h926e7f8_0 conda-forge
>> libblas 3.9.0 8_openblas conda-forge
>> libcblas 3.9.0 8_openblas conda-forge
>> libcurl 7.76.1 hc4aaa36_1 conda-forge
>> libdap4 3.20.6 hd7c4107_2 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 11.1.0 hc902ee8_6 conda-forge
>> libgdal 3.1.4 h50e41a3_1 conda-forge
>> libgfortran-ng 7.5.0 h14aa051_19 conda-forge
>> libgfortran4 7.5.0 h14aa051_19 conda-forge
>> libglib 2.68.3 h3e27bee_0 conda-forge
>> libgomp 11.1.0 hc902ee8_6 conda-forge
>> libiconv 1.16 h516909a_0 conda-forge
>> libkml 1.3.0 h238a007_1014 conda-forge
>> libnetcdf 4.7.4 nompi_h56d31a8_107
>> conda-forge
>> libnghttp2 1.43.0 h812cca2_0 conda-forge
>> libopenblas 0.3.12 pthreads_hb3c22a3_1
>> conda-forge
>> libpng 1.6.37 h21135ba_2 conda-forge
>> libpq 12.3 h255efa7_3 conda-forge
>> librttopo 1.1.0 hb271727_4 conda-forge
>> libspatialite 5.0.1 h6ec7341_0 conda-forge
>> libssh2 1.9.0 ha56f1ee_6 conda-forge
>> libstdcxx-ng 11.1.0 h56837e0_6 conda-forge
>> libtiff 4.2.0 hbd63e13_2 conda-forge
>> libuuid 2.32.1 h7f98852_1000 conda-forge
>> libwebp-base 1.2.0 h7f98852_2 conda-forge
>> libxcb 1.13 h7f98852_1003 conda-forge
>> libxml2 2.9.10 h68273f3_2 conda-forge
>> lz4-c 1.9.3 h9c3ff4c_1 conda-forge
>> ncl 6.6.2 h087f628_23 conda-forge
>> ncurses 6.2 h58526e2_4 conda-forge
>> netcdf-fortran 4.5.3 nompi_hfef6a68_101
>> conda-forge
>> openjpeg 2.4.0 hb52868f_1 conda-forge
>> openssl 1.1.1k h7f98852_0 conda-forge
>> pcre 8.45 h9c3ff4c_0 conda-forge
>> pixman 0.38.0 h516909a_1003 conda-forge
>> poppler 0.89.0 h2de54a5_5 conda-forge
>> poppler-data 0.4.10 0 conda-forge
>> postgresql 12.3 hc2f5b80_3 conda-forge
>> proj 7.1.1 h966b41f_3 conda-forge
>> pthread-stubs 0.4 h36c2ea0_1001 conda-forge
>> readline 8.1 h46c0cb4_0 conda-forge
>> sqlite 3.36.0 h9cd32fc_0 conda-forge
>> tiledb 2.1.6 h91fcb0e_1 conda-forge
>> tk 8.6.10 h21135ba_1 conda-forge
>> tzcode 2021a h7f98852_2 conda-forge
>> udunits2 2.2.27.27 h975c496_1 conda-forge
>> xerces-c 3.2.3 hfe33f54_1 conda-forge
>> xorg-imake 1.0.7 0 conda-forge
>> xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
>> xorg-libice 1.0.10 h7f98852_0 conda-forge
>> xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
>> xorg-libx11 1.6.12 h36c2ea0_0 conda-forge
>> xorg-libxau 1.0.9 h7f98852_0 conda-forge
>> xorg-libxaw 1.0.14 h7f98852_0 conda-forge
>> xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
>> xorg-libxext 1.3.4 h516909a_0 conda-forge
>> xorg-libxmu 1.1.3 h516909a_0 conda-forge
>> xorg-libxpm 3.5.13 h516909a_0 conda-forge
>> xorg-libxrender 0.9.10 h516909a_1002 conda-forge
>> xorg-libxt 1.1.5 h516909a_1003 conda-forge
>> xorg-makedepend 1.0.6 he1b5a44_1 conda-forge
>> xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
>> xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
>> xorg-xproto 7.0.31 h7f98852_1007 conda-forge
>> xz 5.2.5 h516909a_1 conda-forge
>> zlib 1.2.11 h516909a_1010 conda-forge
>> zstd 1.4.9 ha95c52a_0 conda-forge
>>
>>
>> 2. After conda activate
>>
>> home/conda/feedstock_root/build_artifacts/ncl_1602173391809/_build_env/bin/x86_64-conda-linux-gnu-gfortran
>> -fPIC -fno-second-underscore -fno-range-check -fopenmp -O
>> -L/home/simon/anaconda3/envs/ncl_stable/lib -Wl,-O2 -Wl,--sort-common
>> -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags
>> -Wl,--gc-sections -Wl,-rpath,/home/simon/anaconda3/envs/ncl_stable/lib
>> -Wl,-rpath-link,/home/simon/anaconda3/envs/ncl_stable/lib
>> -L/home/simon/anaconda3/envs/ncl_stable/lib maps.f95
>> -L/home/simon/anaconda3/envs/ncl_stable/lib -L/usr/X11R6/lib64 -lncarg
>> -lncarg_gks -lncarg_c -lX11 -lXext -lcairo -lXrender -lfontconfig
>> -lpixman-1 -lfreetype -lexpat -lpng -lz -lbz2
>> /home/conda/feedstock_root/build_artifacts/ncl_1602173391809/_build_env/bin/x86_64-conda-linux-gnu-gfortran:
>> Command not found.
>>
>>
>>
>>
>> On 7/22/21 9:54 AM, Orhan Eroglu wrote:
>>
>> Hi Simon,
>>
>> Could you please provide the he outputs of the following three commands:
>>
>> which ncl
>> ncl -V
>> env | grep NCARG
>>
>> Thanks!
>>
>>
>> On Mon, Jul 19, 2021 at 11:13 AM Simon J Mason via ncl-install <
>> ncl-install at mailman.ucar.edu> wrote:
>>
>>> I have successfully installed NCAR Graphics on ubuntu using anaconda, as
>>>
>>> per the recommendation. The following commands all performed as they
>>> should:
>>>
>>> ncl -V
>>> ncl $NCARG_ROOT/lib/ncarg/nclex/gsun/gsun02n.ncl
>>> ncl $NCARG_ROOT/lib/ncarg/nclex/nug/NUG_multi_timeseries.ncl
>>>
>>> However, if I try to run ncargf90 on this new installation, I get a long
>>> error message
>>> ultimately saying:
>>>
>>> /home/conda/feedstock_root/build_artifacts/ncl_1602173391809/_build_env/bin/x86_64-conda-linux-gnu-gfortran:
>>> Command not found.
>>>
>>> I do not seem to have a /home/conda directory, and am new to Anaconda.
>>>
>>> Please advise.
>>>
>>> Many thanks,
>>>
>>> Simon Mason
>>>
>>>
>>> --
>>> ____________________________________________________________________
>>> Senior Research Scientist
>>> Chief Climate Scientist
>>>
>>> Tel : +1 845 680 4514 IRI, Columbia University
>>> Fax : +1 845 680 4865 61 Route 9W, PO Box 1000
>>> E-mail: simon at iri.columbia.edu Palisades, NY 10964-8000
>>> WWW : http://iri.columbia.edu/contact/staff-directory/simon-mason/
>>>
>>> Ἆρα σύ, ὦ Σώκρατες, ὁ φροντιστὴς ἐπικαλούμενος;
>>> Οὐκοῦν κάλλιον, ἔφη, ἢ εἰ ἀφρόντιστος ἐκαλούμην.
>>> Εἰ μή γε ἐδόκεις τῶν μετεώρων φροντιστὴς εἶναι.
>>>
>>> Xenophon
>>> ____________________________________________________________________
>>>
>>> _______________________________________________
>>> ncl-install mailing list
>>> List instructions, subscriber options, unsubscribe:
>>> https://mailman.ucar.edu/mailman/listinfo/ncl-install
>>
>> --
> ____________________________________________________________________
> Senior Research Scientist
> Chief Climate Scientist
>
> Tel : +1 845 680 4514 IRI, Columbia University
> Fax : +1 845 680 4865 61 Route 9W, PO Box 1000
> E-mail: simon at iri.columbia.edu Palisades, NY 10964-8000
> WWW : http://iri.columbia.edu/contact/staff-directory/simon-mason/
>
> Ἆρα σύ, ὦ Σώκρατες, ὁ φροντιστὴς ἐπικαλούμενος;
> Οὐκοῦν κάλλιον, ἔφη, ἢ εἰ ἀφρόντιστος ἐκαλούμην.
> Εἰ μή γε ἐδόκεις τῶν μετεώρων φροντιστὴς εἶναι.
>
> Xenophon
> ____________________________________________________________________
>
>
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