Hi Nash (and Dan), I started from scratch and reinstalled everything per Dan's instructions, we still get the seg fault unfortunately. I am pretty certain though this is something on our end and not the software, I just need to test the manual build, like Dan suggests, and if that still returns the same error- we'll have to pass this onto the more advanced systems guys here at NCI.
One tiny bit of good news however- I didn't know that part about order mattering with the conda channels. (Thank you Dan- very useful.) This solved one of our hdf4 library conflicts that we had to previously modify. Sorry again Nash that this has been such a painful process. Like I said, I'll do the manual build and then if that still fails- I'll pass it up to others here at NCI. Cheers, Kelsey --- Kelsey A. Druken Earth Systems Data Service Specialist National Computational Infrastructure (NCI) Leonard Huxley Building, Mills Road The Australian National University Canberra ACT 0200 Australia E: kelsey.dru...@anu.edu.au T: +61 2 6125 2479 W: nci.org.au On Fri, Aug 19, 2016 at 9:44 PM, Daniel Clewley <daniel.clew...@gmail.com> wrote: > Hi Narsimha, > > I think the problem is some packages from the osgeo channel are being > pulled in but it should be using ones from conda-forge. Try: > > conda clean --tar --packages --yes > conda create -n spdlib_condaforge -c conda-forge -c rios -c osgeo > spdlib=3.3 > > Note the conda-forge channel is passed in first (this is important with > the latest version of conda, which I only found out recently). > > The only package pulled in from osgeo should be spdlib. > If you still have problems try removing and reinstalling miniconda then > running the commands above again. > > This is as stable a build as we have available. Note if you want a more > stable build you may wish to build all the packages from source rather than > relying on the conda packages. > > Thanks, > > Dan > > > > On 19 August 2016 at 12:19, Narsimha Garlapati < > narsimha.garlap...@anu.edu.au> wrote: > >> Hi Dan, >> >> >> >> I have several versions of LAS data (1.2,1.3 and 1.4) and would like to >> process them. >> >> >> >> I’m using a virtual desktop with Gnome terminal and I think it’s a Centos >> OS. >> >> >> >> Below is the conda list from my new installations. Another colleague from >> Adam’s team is also experiencing the similar “seg errors”. >> >> >> >> So far we are unable to troubleshoot this problem, when you get a chance >> can you please provide us some suggestions so that we can create a stable >> version. >> >> >> >> >> >> (spdlib) [nxg650@vdi-n16 ~]$ conda list >> >> # packages in environment at /g/data1/xc0/user/Garlapati/mi >> niconda3/envs/spdlib: >> >> # >> >> cairo 1.12.18 6 >> >> boost 1.61.0 py35_1 conda-forge >> >> cgal 4.8.1 py35_0 conda-forge >> >> curl 7.49.1 0 conda-forge >> >> expat 2.1.0 1 conda-forge >> >> freexl 1.0.2 1 conda-forge >> >> gdal 2.1.1 np111py35_1 conda-forge >> >> giflib 5.1.2 1 conda-forge >> >> hdf5 1.8.17 2 conda-forge >> >> icu 56.1 4 conda-forge >> >> jpeg 9b 0 conda-forge >> >> json-c 0.12 0 conda-forge >> >> kealib 1.4.6 3 conda-forge >> >> libdap4 3.18.0 2 conda-forge >> >> libiconv 1.14 3 conda-forge >> >> libnetcdf 4.4.0 2 conda-forge >> >> libpng 1.6.23 0 conda-forge >> >> libspatialite 4.3.0a 9 conda-forge >> >> libtiff 4.0.6 6 conda-forge >> >> libuuid 1.0.3 1 conda-forge >> >> libxml2 2.9.4 0 conda-forge >> >> postgresql 9.5.3 2 conda-forge >> >> proj.4 4.9.2 0 conda-forge >> >> fontconfig 2.11.1 6 >> >> freetype 2.5.5 1 >> >> glib 2.43.0 1 >> >> harfbuzz 0.9.39 1 >> >> libffi 3.2.1 0 >> >> mkl 11.3.3 0 >> >> numpy 1.11.1 py35_0 >> >> openssl 1.0.2h 1 >> >> geos 3.4.2 0 osgeo >> >> gmp 5.1.2 0 osgeo >> >> gsl 2.1 2 osgeo >> >> hdf4 4.2.11 3 osgeo >> >> mpfr 3.1.2 0 osgeo >> >> openjpeg 2.1.0 0 osgeo >> >> spdlib 3.3.0 0 osgeo >> >> tuiview 1.1.8 py35_1 osgeo >> >> xerces-c 3.1.1 0 osgeo >> >> pango 1.39.0 1 >> >> pip 8.1.2 py35_0 >> >> pixman 0.32.6 0 >> >> pyqt 4.11.4 py35_4 >> >> python 3.5.2 0 >> >> qt 4.8.7 4 >> >> readline 6.2 2 >> >> lastools 20160606 0 rios >> >> setuptools 25.1.6 py35_0 >> >> sip 4.18 py35_0 >> >> sqlite 3.13.0 0 >> >> tk 8.5.18 0 >> >> wheel 0.29.0 py35_0 >> >> xz 5.2.2 0 >> >> zlib 1.2.8 3 >> >> >> >> Regards, >> >> Nash >> >> *From: *Daniel Clewley <daniel.clew...@gmail.com> >> *Date: *Wednesday, 17 August 2016 at 10:34 PM >> *To: *Narsimha Garlapati <narsimha.garlap...@anu.edu.au> >> *Cc: *spdlib-develop <spdlib-develop@lists.sourceforge.net> >> *Subject: *Re: seg fault to wkt file errors >> >> >> >> Hi Narsimha, >> >> >> >> This is a problem with how you are calling the command. You have ‘-i’ >> followed by ‘--input_proj’, rather than the input. This is interpreted as >> having the input as ‘--input_proj’, then you are using ‘GDA94MGAZn55.wkt’ >> as an argument without a flag. >> >> >> >> Also it needs to be a file not a web address. >> >> >> >> As for reverting to a previous version from an earlier email I was under >> the impression you needed LAS 1.3 support which is only available in the >> latest version (hence why you needed the Linux version not the old Windows >> version). >> >> >> >> For the seg fault, I’m not sure why this is happening. Are you sure there >> isn’t a problem with the input file? Do you have read access to the input >> file and write access to where you are trying to write to? If it was >> working before on the same file in the same location can you provide me >> details of your system (OS etc.,) also the outputs of: >> >> >> >> conda list >> >> >> >> At the moment you haven’t provided much information to go on. >> >> >> >> Thanks, >> >> >> >> Dan >> >> >> >> On 17 Aug 2016, at 12:40, Narsimha Garlapati < >> narsimha.garlap...@anu.edu.au> wrote: >> >> >> >> Hi Dan, >> >> >> >> I have tried to input wkt files in various formats and getting the >> following errors. >> >> >> >> (spdlib) [nxg650@vdi-n4 AHD]$ spdtranslate --if LAS --of SPD -b 10 -x >> LAST_RETURN -i --input_proj GDA94MGAZn55.wkt -i 687000-6092000.las -o >> lidartest.spd >> >> >> >> >> >> PARSE ERROR: Argument: GDA94MGAZn55.*wkt* >> >> Couldn't find match for argument >> >> >> >> PARSE ERROR: Argument: GDA94MGAZn55.t*xt* >> >> Couldn't find match for argument >> >> >> >> PARSE ERROR: Argument: *http://spatialreference.org/ref/epsg/28355/ogcwkt >> <http://spatialreference.org/ref/epsg/28355/ogcwkt>* >> >> Couldn't find match for argument >> >> >> >> Please let me know if I’m going wrong somewhere, by the way do you think >> is it better to revert to a previous stable version? >> >> >> >> Happy to seek your feedback, >> >> >> >> Thanks, >> >> Nash >> >> >> >> *From: *Daniel Clewley <daniel.clew...@gmail.com> >> *Date: *Wednesday, 17 August 2016 at 4:27 PM >> *To: *Narsimha Garlapati <narsimha.garlap...@anu.edu.au> >> *Cc: *spdlib-develop <spdlib-develop@lists.sourceforge.net> >> *Subject: *Re: [spdlib-develop] segmentation fault? >> >> >> >> Hi Narsimha, >> >> >> >> From my earlier email: >> >> >> >> You will also need to pass in the projection as a WKT file using >> --input_proj as it is currently segfaulting when trying to read the >> projection from a LAS 1.4 file. >> >> >> >> Is this a LAS 1.4 file? If so you need to pass in a text file containing >> the projection in WKT format using the --input_proj flag. >> >> If you don’t already have a WKT file you can download one from >> http://spatialreference.org/ >> >> >> >> Thanks, >> >> >> >> Dan >> >> On 17 Aug 2016, at 05:26, Narsimha Garlapati < >> narsimha.garlap...@anu.edu.au> wrote: >> >> >> >> Hi Dan, >> >> Finally with the kind support from NCI, I have managed to install the >> latest spdlib. >> >> To test the new installation I have tried to run a spdtranslate and >> experiencing the “segmentation fault” error? >> >> Below is the error message, any suggestions to overcome this? >> >> >> >> (spdlib) [nxg650@vdi-n6 las]$ spdtranslate --if LAS --of SPD -b 10 -x >> LAST_RETURN -i /g/data1/xc0/user/Garlapati/AHD/las/687000-6092000.las -o >> lidartest.spd >> >> spdtranslate SPDLib 3.3.309, Copyright (C) 2016 Sorted Pulse Library (SPD) >> >> This program comes with ABSOLUTELY NO WARRANTY. This is free software, >> >> and you are welcome to redistribute it under certain conditions; See >> >> website (http://www.spdlib.org). Bugs are to be reported on the trac >> >> or directly to spdlib-develop@lists.sourceforge.net >> >> Segmentation fault >> >> >> >> >> >> Regards, >> >> Narsimha >> >> >> >> >> >> ------------------------------------------------------------ >> ------------------ >> _______________________________________________ >> spdlib-develop mailing list >> spdlib-develop@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/spdlib-develop >> >> >> >> >> > >
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