re-running carrel errors and wipes out index.htm

[nkmeyers]

I re-ran carrel SusceptibilityTwo by going to the carrel and running sudo sbatch make-carrrel.slurm as job 2711 and then

goodnews: it completed super fast (3:05) and badnews: it wiped out my index.htm to 0 bytes.

Can you check it out and try to re-run? maybe take a look at my standard-error.txt which has a bunch of FileNotFoundErrors like “FileNotFoundError: File b’./tsv/trigrams.tsv’ does not exist” and the error file starts like this: Initializing database /export/reader/bin/cord2carrel.sh: line 46: parallel: command not found Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named SusceptibilityTwo Jun 27, 2020 11:00:48 PM org.apache.tika.config.InitializableProblemHandler$3 handleInitializableProblem WARNING: J2KImageReader not loaded. JPEG2000 files will not be processed. See https://pdfbox.apache.org/2.0/dependencies.html#jai-image-io for optional dependencies.

Jun 27, 2020 11:00:49 PM org.apache.tika.config.InitializableProblemHandler$3 handleInitializableProblem WARNING: org.xerial’s sqlite-jdbc is not loaded. Please provide the jar on your classpath to parse sqlite files. See tika-parsers/pom.xml for the correct version. INFO Starting Apache Tika 1.22 server INFO Setting the server’s publish address to be http://localhost:9998/ INFO Logging initialized @7980ms to org.eclipse.jetty.util.log.Slf4jLog INFO jetty-9.4.z-SNAPSHOT; built: 2019-04-29T20:42:08.989Z; git: e1bc35120a6617ee3df052294e433f3a25ce7097; jvm 1.8.0_201-b09 INFO Started ServerConnector@a078fd{HTTP/1.1,[http/1.1]}{localhost:9998} INFO Started @8134ms WARN Empty contextPath INFO Started o.e.j.s.h.ContextHandler@7a164b{/,null,AVAILABLE} INFO Started Apache Tika server at http://localhost:9998/ Que is empty; done SusceptibilityTwo

[ericleasemorgan]

On Jun 27, 2020, at 7:19 PM, Natalie Meyers notifications@github.com wrote:

/export/reader/bin/cord2carrel.sh: line 46: parallel: command not found

The error, above, leads me to believe your path is not complete. Let's try a test:

1) Copy the attached file to your home directory on the head node (149.165.170.42) and make sure the file's name is .bash_profile. I'm assuming your shell is bash, and remember, save it in your home directory.

2) Log out.

3) Log back in to the head node (149.165.170.42).

4) Change directories (cd /export/reader/carrels/SusceptibilityTwo).

5) Re-run the carrel (sbatch ./make-carrel.slurm).

6) Tell me what happens.

You & I are the only "users" creating carrels, so the path thing has not been implemented system-wide.

-- Eric

[ericleasemorgan]

Here is the .bash_profile, attached as bash_profile.txt

bash_profile.txt

[nkmeyers]

yeah, my .bash_profile is currently:

.bash_profile

Get the aliases and functions

if [ -f ~/.bashrc ]; then

. ~/.bashrc

fi

User specific environment and startup programs

PATH=$PATH:$HOME/.local/bin:$HOME/bin

export PATH

On Mon, Jun 29, 2020 at 3:29 PM Eric Lease Morgan notifications@github.com wrote:

Here is the .bash_profile, attached as bash_profile.txt

bash_profile.txt https://github.com/ericleasemorgan/reader/files/4847622/bash_profile.txt

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ericleasemorgan/reader/issues/121#issuecomment-651314303, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAXHLEVVCU5PKAHIIV2XS5LRZDTPZANCNFSM4OKHVGFA .

-- Natalie K. Meyers E-Research Librarian & Acting Director Navari Family Center for Digital Scholarship

Hesburgh Libraries

University of Notre Dame 250-D Hesburgh Library Notre Dame, IN 46556 o: 574-631-1546 f: 574-631-6772 w: cds.library.nd.edu e: natalie.meyers@nd.edu

ORCID: https://orcid.org/0000-0001-6441-6716 Book a Meeting with Me - https://doodle.com/mm/nataliemeyers/book-a-time

[nkmeyers]

Ok, updated my bash profile and logged out and back in and re-ran make-carrel.slurm on SusceptibilityTwo as job 2713 that failed. trying again w sudo as job 2714. It completed .