[ncl-talk] [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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