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I-TASSER standalone errors

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I-TASSER standalone errors

Posted: Wed Mar 20, 2024 2:16 am
by 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?

Re: I-TASSER standalone errors

Posted: Wed Mar 20, 2024 3:43 am
by 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

***Need developer help*** I-TASSER standalone errors

Posted: Wed Mar 27, 2024 2:55 am
by harvey@bucknell.edu
Are any devs able to provide insight on my issues?

Re: I-TASSER standalone errors

Posted: Wed Aug 27, 2025 10:02 pm
by cenat
For the Java errors, it looks like the job script might still be pointing to a wrong or missing directory, or there’s something odd with the input format. I’d suggest checking your paths and making sure all required input files are clean and readable. Also confirm you’re using a Java version that matches I-TASSER requirements.nulls brawl indir

Re: I-TASSER standalone errors

Posted: Thu Aug 28, 2025 3:07 pm
by blazesimilar
harvey@bucknell.edu wrote: ↑Wed Mar 20, 2024 2:16 am 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?
These errors usually come from two issues: (1) the working directory `/tmp/harvey/ITexample2` doesn’t exist or isn’t created on compute nodes, so SLURM falls back to `/tmp`—fix by making sure your job script creates and uses a writable working dir (e.g. `$SLURM_TMPDIR` or a directory in your home/scratch) and runs I-TASSER there; (2) the “-NAN” NumberFormatException is often downstream of missing/failed alignment or threading results caused by the bad working directory or missing dependencies. In practice, run the example from a stable location (not `/tmp`), confirm all required databases and environment variables are accessible on compute nodes, and check that Java and Perl versions match I-TASSER requirements.
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