[ncl-install] ncl_convert2nc ncl_filedump not working segmentation fault

Dennis Shea shea at ucar.edu
Mon Jun 17 09:21:36 MDT 2019


The 'fix' suggested by Rick Brownrigg:
===
I might add that we have been getting recent reports of ncl_filedump
SEGV-ing on Ubuntu systems. We don't have access at the moment to such a
system to verify and track down the problem. However, as I recall, the
issue is related to the C-shell (csh) on those systems (ncl_filedump is
actually a C-shell script that ultimately calls into NCL to do the work).
If your system is indeed Ubuntu, a work-around seems to be to use the
tahoe-shell instead (tcsh).  *That can be done by editing ncl_filedump,
replacing the first line:*

*    #!/bin/csh -f*


*with *

*   #!/bin/tcsh -f*

---
*Also, for ncl_convert2nc and WRAPIT*

On Wed, Jun 12, 2019 at 6:44 AM Jing Tang via ncl-install <
ncl-install at ucar.edu> wrote:

> Hi,
>
> I am trying to use ncl to convert some of downloaded MODIS hdf file to
> nc.  Please see the error message below.
>
> The same error when I type ncl_filedump or ncl_convert2nc
>
>
>
> *>ncl_convert2nc MCD12Q1.A2012001.h18v01.006.2018055002712.hdf Processing
> file: MCD12Q1.A2012001.h18v01.006.2018055002712.hdf...Segmentation fault
> (core dumped)*
>
> I used conda installed ncl, and had no problem when running these test
> command after installation.
>
> >ncl $NCARG_ROOT/lib/ncarg/nclex/gsun/gsun02n.ncl
>
> >ncl $NCARG_ROOT/lib/ncarg/nclex/nug/NUG_multi_timeseries.ncl
>
>
>
>
>
> Here are the required information:
>
>
> >conda list -n *ncl_stable*
>
>  # packages in environment at /home/jing/miniconda2/envs/ncl_stable:
> #
> # Name                    Version                   Build  Channel
> boost-cpp                 1.68.0            h11c811c_1000    conda-forge
> bzip2                     1.0.6             h14c3975_1002    conda-forge
> ca-certificates           2019.3.9             hecc5488_0    conda-forge
> cairo                     1.16.0            ha4e643d_1000    conda-forge
> certifi                   2019.3.9                 py37_0    conda-forge
> cfitsio                   3.430             h0bd2449_1002    conda-forge
> cftime                    1.0.3.4         py37hd352d35_1001    conda-forge
> curl                      7.64.1               hf8cf82a_0    conda-forge
> esmf                      7.1.0             hdfb41a0_1004    conda-forge
> expat                     2.2.5             hf484d3e_1002    conda-forge
> fontconfig                2.13.1            he4413a7_1000    conda-forge
> freetype                  2.10.0               he983fc9_0    conda-forge
> freexl                    1.0.5             h14c3975_1002    conda-forge
> geos                      3.7.1             hf484d3e_1000    conda-forge
> geotiff                   1.5.1                h560c3f3_2    conda-forge
> gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
> giflib                    5.1.7                h516909a_1    conda-forge
> glib                      2.58.3            hf63aee3_1001    conda-forge
> gsl                       2.4               h294904e_1006    conda-forge
> hdf4                      4.2.13            h9a582f1_1002    conda-forge
> hdf5                      1.10.4          nompi_h3c11f04_1106
>  conda-forge
> hdfeos2                   2.20              h64bfcee_1000    conda-forge
> hdfeos5                   5.1.16               hccfc538_4    conda-forge
> icu                       58.2              hf484d3e_1000    conda-forge
> jasper                    1.900.1           h07fcdf6_1006    conda-forge
> jpeg                      9c                h14c3975_1001    conda-forge
> json-c                    0.13.1            h14c3975_1001    conda-forge
> kealib                    1.4.10            h1978553_1003    conda-forge
> krb5                      1.16.3            h05b26f9_1001    conda-forge
> libblas                   3.8.0               10_openblas    conda-forge
> libcblas                  3.8.0               10_openblas    conda-forge
> libcurl                   7.64.1               hda55be3_0    conda-forge
> libdap4                   3.19.1            hd48c02d_1000    conda-forge
> libedit                   3.1.20170329      hf8c457e_1001    conda-forge
> libffi                    3.2.1             he1b5a44_1006    conda-forge
> libgcc-ng                 8.2.0                hdf63c60_1
> libgdal                   2.4.1                h02bbc0b_3    conda-forge
> libgfortran-ng            7.3.0                hdf63c60_0
> libiconv                  1.15              h516909a_1005    conda-forge
> libkml                    1.3.0             h328b03d_1009    conda-forge
> liblapack                 3.8.0               10_openblas    conda-forge
> libnetcdf                 4.6.2             hbdf4f91_1001    conda-forge
> libpng                    1.6.37               hed695b0_0    conda-forge
> libpq                     11.3                 h4e4e079_0    conda-forge
> libspatialite             4.3.0a            h4c5cd43_1028    conda-forge
> libssh2                   1.8.2                h22169c7_2    conda-forge
> libstdcxx-ng              8.2.0                hdf63c60_1
> libtiff                   4.0.10            h648cc4a_1001    conda-forge
> libuuid                   2.32.1            h14c3975_1000    conda-forge
> libxcb                    1.13              h14c3975_1002    conda-forge
> libxml2                   2.9.9                h13577e0_0    conda-forge
> lz4-c                     1.8.3             he1b5a44_1001    conda-forge
> mpi                       1.0                       mpich    conda-forge
> mpich                     3.2.1             hc99cbb1_1009    conda-forge
> ncl                       6.6.2                h3a5803f_3    conda-forge
> nco                       4.8.0                hfb3d286_0    conda-forge
> ncurses                   6.1               hf484d3e_1002    conda-forge
> netcdf-fortran            4.4.5             hea25ff8_1000    conda-forge
> netcdf4                   1.5.1.2          py37had58050_0    conda-forge
> numpy                     1.16.4           py37h95a1406_0    conda-forge
> openblas                  0.3.6                h6e990d7_2    conda-forge
> openjpeg                  2.3.1                h58a6597_0    conda-forge
> openssl                   1.1.1b               h14c3975_1    conda-forge
> pcre                      8.41              hf484d3e_1003    conda-forge
> pip                       19.1                     py37_0    conda-forge
> pixman                    0.34.0            h14c3975_1003    conda-forge
> poppler                   0.67.0               h2ad7f00_6    conda-forge
> poppler-data              0.4.9                         1    conda-forge
> postgresql                11.3                 hbeee2d4_0    conda-forge
> proj4                     6.1.0                he751ad9_2    conda-forge
> pthread-stubs             0.4               h14c3975_1001    conda-forge
> python                    3.7.3                h5b0a415_0    conda-forge
> readline                  7.0               hf8c457e_1001    conda-forge
> setuptools                41.0.1                   py37_0    conda-forge
> sqlite                    3.28.0               h8b20d00_0    conda-forge
> tempest-remap             2.0.3                h5f743cb_0    conda-forge
> tk                        8.6.9             h84994c4_1001    conda-forge
> tzcode                    2019a             h516909a_1002    conda-forge
> udunits2                  2.2.27.6          h4e0c4b3_1001    conda-forge
> wheel                     0.33.4                   py37_0    conda-forge
> xerces-c                  3.2.2             hac72e42_1001    conda-forge
> xorg-imake                1.0.7                         0    conda-forge
> xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
> xorg-libice               1.0.9             h516909a_1004    conda-forge
> xorg-libsm                1.2.3             h84519dc_1000    conda-forge
> xorg-libx11               1.6.7             h14c3975_1000    conda-forge
> xorg-libxau               1.0.9                h14c3975_0    conda-forge
> xorg-libxaw               1.0.13            h14c3975_1002    conda-forge
> xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
> xorg-libxext              1.3.4                h516909a_0    conda-forge
> xorg-libxmu               1.1.3                h516909a_0    conda-forge
> xorg-libxpm               3.5.12            h14c3975_1002    conda-forge
> xorg-libxrender           0.9.10            h516909a_1002    conda-forge
> xorg-libxt                1.1.5             h14c3975_1002    conda-forge
> xorg-makedepend           1.0.6                he1b5a44_1    conda-forge
> xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
> xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
> xorg-xproto               7.0.31            h14c3975_1007    conda-forge
> xz                        5.2.4             h14c3975_1001    conda-forge
> zlib                      1.2.11            h14c3975_1004    conda-forge
> zstd                      1.4.0                h3b9ef0a_0    conda-forge
> >conda --version
>
> conda 4.6.14
> >ncl -V
> 6.6.2
>
>
>  >which ncl
> /home/jing/miniconda2/envs/ncl_stable/bin/ncl
>
>  >env | grep NCARG
> OLD_NCARG_ROOT=/home/jing/miniconda2/envs/ncl_stable:
> NCARG_ROOT=/home/jing/miniconda2/envs/ncl_stable
>
>
> Looking forward to your suggestions!
>
>
> Best regards, Jing
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