Script issue

[Daniel Berman]

I've been successfully using David Mayer's scripts on my old system, and I recently set up a new VM to run ASP and ISIS. The programs run fine from the command line, but when I try to run a script, I get an error saying it couldn't find the ISIS program, and it's looking in the StereoPipeline bin for some reason. Example:

 **I/O ERROR** Unable to open [/home/bermandc/StereoPipeline-3.4.0-2024-06-19-x86_64-Linux/bin/xml/hi2isis.xml]

I was able to solve this problem in a previous VM by making sure I had all of the correct PATHs in my .bashrc, but that's not working now.

[Oleg Alexandrov]

For ISIS programs, you may need to set ISISROOT to point to the base of your ISIS install dir. Then prepend to the PATH the ISIS install bin directory, or specify the full path to the tool you want to run. 

If that does not fix it, I hope you can share more details, such as what tool is failing. 

If it runs from the command line, but not from a script you can try to compare the value of the "env" command in the two situations (so can be added to the script, before the tool runs).

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[Daniel Berman]

The env results look identical, and I have the correct path. All isis tools run fine on the command line, and none work in the script. It's frustrating, because the script worked before, and my VM got corrupted and had to be rebuilt, and now I'm having this issue when everything is set up identically. This script, for example, just runs all os the ISIS processing on a CTX pair and I'm getting these errors:

 **I/O ERROR** Unable to open [/home/bermandc/StereoPipeline-3.4.0-2024-06-19-x86_64-Linux/bin/xml/mroctx2isis.xml].

**I/O ERROR** Unable to open [/home/bermandc/StereoPipeline-3.4.0-2024-06-19-x86_64-Linux/bin/xml/mroctx2isis.xml].
**I/O ERROR** Unable to open [/home/bermandc/StereoPipeline-3.4.0-2024-06-19-x86_64-Linux/bin/xml/spiceinit.xml].
**I/O ERROR** Unable to open [/home/bermandc/StereoPipeline-3.4.0-2024-06-19-x86_64-Linux/bin/xml/spiceinit.xml].
**I/O ERROR** Unable to open [/home/bermandc/StereoPipeline-3.4.0-2024-06-19-x86_64-Linux/bin/xml/spicefit.xml].
**I/O ERROR** Unable to open [/home/bermandc/StereoPipeline-3.4.0-2024-06-19-x86_64-Linux/bin/xml/spicefit.xml].
**I/O ERROR** Unable to open [/home/bermandc/StereoPipeline-3.4.0-2024-06-19-x86_64-Linux/bin/xml/ctxcal.xml].
**I/O ERROR** Unable to open [/home/bermandc/StereoPipeline-3.4.0-2024-06-19-x86_64-Linux/bin/xml/ctxcal.xml].
**I/O ERROR** Unable to open [/home/bermandc/StereoPipeline-3.4.0-2024-06-19-x86_64-Linux/bin/xml/ctxevenodd.xml].
**I/O ERROR** Unable to open [/home/bermandc/StereoPipeline-3.4.0-2024-06-19-x86_64-Linux/bin/xml/ctxevenodd.xml].

I can't understand for the life of me why it's looking in that directory for the ISIS programs. Even if I take the path to the StereoPipeline directory out of my .bashrc, it still does this.

--

Daniel C. Berman

Senior Scientist

Planetary Science Institute

[Oleg Alexandrov]

Your script has nothing to do with ASP, as it looks. It is ISIS preprocessing work.

Where does your ISIS come from? ASP ships the ASP libs but not ASP itself. 

Or maybe you installed ASP and conda in same env? That should not be a problem, but maybe something bleeds over.

Does tyinging "env" bring up any ASP-related info?

You can just wipe ASP and ISIS, get a fresh ISIS with conda, and rerun. Later, can bring back ASP in a different env or subdir, and not set any ASP-related env, but use full paths to the ASP programs.

[Oleg Alexandrov]

Correcting a couple of typos: 1. Maybe you have ASP and ISIS in same conda env. (Should not be a problem but go figure.) 2. The ASP taraball installs ISIS libs but not ISIS itself.

[Daniel Berman]

This one is just pre-processing, the others are for ASP. I have ISIS installed in a conda env and it runs fine from the command line. ASP is installed in my home directory, and it runs fine too. It's just the scripts. These are the scripts from David Mayer's github that run CTX and HiRISE pairs. They've always worked fine for me before. I'm talking with my IT staff.