I-TASSER standalone errors

[harvey@bucknell.edu]

I have been trying to get I-TASSER standalone working on a Rocky Linux 8 SLURM cluster. I've been able to run the included example with some success, but a few of the threading processes fail with the following errors:

err_MUSTER_example2
::::::::::::::
slurmstepd: error: couldn't chdir to `/tmp/harvey/ITexample2': No such file or directory: going to /tmp instead
slurmstepd: error: couldn't chdir to `/tmp/harvey/ITexample2': No such file or directory: going to /tmp instead
Illegal division by zero at /cm/local/apps/slurm/var/spool/job95404/slurm_script line 599.
::::::::::::::

err_wdPPAS_example2
::::::::::::::
slurmstepd: error: couldn't chdir to `/tmp/harvey/ITexample2': No such file or directory: going to /tmp instead
slurmstepd: error: couldn't chdir to `/tmp/harvey/ITexample2': No such file or directory: going to /tmp instead
Exception in thread "main" java.lang.NumberFormatException: For input string: "-NAN."
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
at sun.misc.FloatingDecimal.parseFloat(FloatingDecimal.java:122)
at java.lang.Float.parseFloat(Float.java:451)
at java.lang.Float.valueOf(Float.java:416)
at c.a(c.java)
at c.main(c.java)
::::::::::::::
err_wMUSTER_example2
::::::::::::::
slurmstepd: error: couldn't chdir to `/tmp/harvey/ITexample2': No such file or directory: going to /tmp instead
slurmstepd: error: couldn't chdir to `/tmp/harvey/ITexample2': No such file or directory: going to /tmp instead
Exception in thread "main" java.lang.NumberFormatException: For input string: "-NAN."
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
at sun.misc.FloatingDecimal.parseFloat(FloatingDecimal.java:122)
at java.lang.Float.parseFloat(Float.java:451)
at java.lang.Float.valueOf(Float.java:416)
at e.a(e.java)
at e.main(e.java)
::::::::::::::


I've seen these errors referenced elsewhere in this forum, but have not seen a solution.

Could anyone provide advice on how to proceed?

[harvey@bucknell.edu]

I believe I have solved the "division by zero" issue by replacing zal* binaries as described in another thread.

I am still, however, seeing the java errors

[harvey@bucknell.edu]

Are any devs able to provide insight on my issues?

[Alice12]

No response on this yet?
word hurdle

[jimmyjane]

Hi Harvey,

I see you’re having some issues running I-TASSER on your SLURM cluster. First, make sure the directory /tmp/harvey/ITexample2 exists. If it doesn’t, you can create it with the command mkdir -p /tmp/harvey/ITexample2. Also, check that you have write permissions for this directory.

Next, verify that all the necessary environment variables for I-TASSER are set up correctly. Sometimes, the "Illegal division by zero" error can occur due to invalid input values, so it’s worth checking your input files as well. Finally, if you’re encountering the NumberFormatException, it might be due to an incompatible Java version, so ensure you’re using a compatible versionthe innocence test

If you still can’t resolve the issue after trying these steps, feel free to share more details about how you’ve configured and run I-TASSER, and others may be able to assist you better.

[emmausa]

This issue typically stems from the data being processed or how it's formatted within I-TASSER's Java components. It could be related to specific input data or a configuration issue. slope