[ncl-install] Fwd: installation tests work but ncargf90 does not run
Orhan Eroglu
oero at ucar.edu
Tue Aug 3 12:08:55 MDT 2021
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
>
>
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