Is it possible to save the output of a bazel build command that is run in terminal? The command is:
bazel build tensorflow/examples/image_retraining:label_image &&
bazel-bin/tensorflow/examples/image_retraining/label_image
--graph=/tmp/output_graph.pb
--labels=/tmp/output_labels.txt
--output_layer=final_result:0
--image=$HOME/Desktop/Image-3/image1.png
I want to save the output to a .txt file; I cannot simply tag on > out.txt to the end of the line or I am thrown an error. But is there bazel-output command?
The stdout of the latest bazel command is logged in your WORKSPACE's output base:
$ echo $(bazel info output_base)
/home/username/.cache/bazel/_bazel_username/3e8af127f8b488324cdf41111355ff4c
and the exact file is command_log:
$ echo $(bazel info command_log)
/home/username/.cache/bazel/_bazel_username/3e8af127f8b488324cdf41111355ff4c/command.log
You can do it by piping the output to both text file and command line, but only on linux. You just append this at the end 2>&1 | tee file_name.log
Related
This is an interesting issue. I have a GitLab project, and I've created a .gitlab-ci.yml to run a PMD that will scan my code after every commit. The ci.yml file looks like this:
image: "node:latest"
stages:
- preliminary-testing
apex-code-scan:
stage: preliminary-testing
allow_failure: false
script:
- install_java
- install_pmd
artifacts:
paths:
- pmd-reports/
####################################################
# Helper Methods
####################################################
.sfdx_helpers: &sfdx_helpers |
function install_java() {
local JAVA_VERSION=11
local JAVA_INSTALLATION=openjdk-$JAVA_VERSION-jdk
echo "Installing ${JAVA_INSTALLATION}"
apt update && apt -y install $JAVA_INSTALLATION
}
function install_pmd() {
local PMD_VERSION=6.52.0
local RULESET_PATH=ruleset.xml
local OUTPUT_DIRECTORY=pmd-reports
local SOURCE_DIRECTORY=force-app
local URL=https://github.com/pmd/pmd/releases/download/pmd_releases%2F$PMD_VERSION/pmd-bin-$PMD_VERSION.zip
# Here I would download and unzip the PMD source code. But for now I have the PMD source already in my project for testing purposes
# apt update && apt -y install unzip
# wget $URL
# unzip -o pmd-bin-$PMD_VERSION.zip
# rm pmd-bin-$PMD_VERSION.zip
echo "Installed PMD!"
mkdir -p $OUTPUT_DIRECTORY
echo "Going to run PMD!"
ls
echo "Start"
pmd-bin-$PMD_VERSION/bin/run.sh pmd -d $SOURCE_DIRECTORY -R $RULESET_PATH -f xslt -P xsltFilename=pmd_report.xsl -r $OUTPUT_DIRECTORY/pmd-apex.html
echo "Done"
rm -r pmd-bin-$PMD_VERSION
echo "Remove pmd"
}
before_script:
- *sfdx_helpers
When I try to run this pipeline, it will fail after starting the PMD:
However, if I make a small change to the PMD's .sh file and add an echo command at the very end. Then the pipeline succeeds:
PMD /bin/run.sh before (doesn't work):
...
java ${HEAPSIZE} ${PMD_JAVA_OPTS} $(jre_specific_vm_options) -cp "${classpath}" "${CLASSNAME}" "$#"
PMD /bin/run.sh after (does work):
...
java ${HEAPSIZE} ${PMD_JAVA_OPTS} $(jre_specific_vm_options) -cp "${classpath}" "${CLASSNAME}" "$#"
echo "Done1" // This is the last line in the file
I don't have the slightest idea why this is the case. Does anyone know why adding this echo command at the end of the .sh file would cause the pipeline to succeed? I could keep it as is with the echo command, but I would like to understand why it is behaving this way. I don't want to be that guy that just leaves a comment saying Hey don't touch this line of code, I don't know why, but without it the whole thing fails. Thank you!
PMD exits with a specific exit code depending whether it found some violations or not, see https://pmd.github.io/latest/pmd_userdocs_cli_reference.html#exit-status
I guess, your PMD run finds some violations, and PMD exits with exit code 4 - which is not a success exit code.
In general, this is used to make the CI build fail, in case any PMD violations are present - forcing to fix the violations before you get a green build.
If that is not what you want, e.g. you only want to report the violations but not fail the build, then you need to add the following command line option:
--fail-on-violation false
Then PMD will exit with exit code 0, even when there are violations.
So it appears that the java command that the PMD runs for some reason returns a non-zero exit code (even though the script is successful). Because I was adding an echo command at the end of that bash script, the last line in the script returned a success exit code, which is why the GitLab CI pipeline succeeded when the echo command was there.
In order to work around the non-zero exit code being returned by the java PMD command, I have changed this line in my .gitlab-ci.yml file to catch the non-zero exit code and proceed.
function install_pmd() {
// ... For brevity I'm just including the line that was changed in this method
pmd-bin-$PMD_VERSION/bin/run.sh pmd -d $SOURCE_DIRECTORY -R $RULESET_PATH -f xslt -P xsltFilename=pmd_report.xsl -r $OUTPUT_DIRECTORY/pmd-apex.html || echo "PMD Returned Exit Code"
// ...
}
My problem is that I have a cluster-server with Torque PBS and want to use it to run a sequence-comparison with the program rapsearch.
The normal RapSearch command is:
./rapsearch -q protein.fasta -d database -o output -e 0.001 -v 10 -x t -z 32
Now I want to run it with 2 nodes on the cluster-server.
I've tried with: echo "./rapsearch -q protein.fasta -d database -o output -e 0.001 -v 10 -x t -z 32" | qsub -l nodes=2 but nothing happened.
Do you have any suggestions? Where I'm wrong? Help please.
Standard output (and error output) files are placed in your home directory by default; take a look. You are looking for a file named STDIN.e[numbers], it will contain the error message.
However, I see that you're using ./rapsearch but are not really being explicit about what directory you're in. Your problem is therefore probably a matter of changing directory into the directory that you submitted from. When your terminal is in the directory of the rapsearch executable, try echo "cd \$PBS_O_WORKDIR && ./rapsearch [arguments]" | qsub [arguments] to submit your job to the cluster.
Other tips:
You could add rapsearch to your path if you use it often. Then you can use it like a regular command anywhere. It's a matter of adding the line export PATH=/full/path/to/rapsearch/bin:$PATH to your .bashrc file.
Create a submission script for use with qsub. Here is a good example.
I am trying to install sqlplus on my mac following the tutorial here: https://tomeuwork.wordpress.com/2014/05/12/how-to-install-oracle-sqlplus-and-oracle-client-in-mac-os/comment-page-1/#comment-6
I have downloaded the two packages (basic and sqlplus) and created all the directories as it says, I moved the necessary files inside the directories.
I created and copied the tnsnames.ora file with the contents:
MYDB=
(DESCRIPTION=
(ADDRESS=
(PROTOCOL=TCP)
(HOST=*********)
(PORT=1521)
)
(CONNECT_DATA=
(SERVER=dedicated)
(SID=MYDB-SID)
) )
And i created the .bash_profile as it says in the tutorial.
But what im stuck on is making the sqlplus run.
typing in sqlplus returns command not found.
in the tutorial it says i should use $ sqlplus username/password#database
where do i get the username and database name from?, I haven't created one yet.
Thanks in advance.
According to your article, you should do the following:
$ vi ~/.bash_profile
Add the following line to the end of the file.
alias sqlplus=’rlwrap sqlplus’
Now reload the .bash_profile:
$ source ~/.bash_profile
Looks like you missed these steps.
You can try to execute:
$rlwrap sqlplus
According to the comments below you do not have sqlplus in the $PATH.
The value of $PATH looks wrong to me: duplicates, quotes.
Option 1
Execute:
export PATH=/Applications/oracle/product/instantclient_64/11.2.0.4.0/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
Then execute in the same console:
$ sqlplus (or $ rlwrap sqlplus)
It will set value only for the current shell. The main idea is to have full path to the sqlplus binary in the $PATH.
Option 2
Modify ~/.bash_profile.
To save as a permanent environment variable edit ~/.bash_profile. There are some details about setting PATH in the source article.
Top down troubleshooting approach
Look for binary - use type
[bbrandt] ~/ $ type sqlplus
sqlplus is aliased to `rlwrap sqlplus'
Where is my binary.. hidden behind an alias, let's unalias
[bbrandt] ~/ $ unalias sqlplus
[bbrandt] ~/ $ type sqlplus
sqlplus is /u01/app/oracle/product/11.2.0/xe/bin/sqlplus
Found it! What happens if I modify my binary search-path?
[bbrandt] ~/ $ echo $PATH
/u01/app/oracle/product/11.2.0/xe/bin:/home/bbrandt/bin:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin
[bbrandt] ~/ $ export PATH=/home/bbrandt/bin:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin
Now, where is my binary?
[bbrandt] ~/ $ type sqlplus
bash: type: sqlplus: not found
[bbrandt] ~/ $
This is where you are... look in your $PATH variable
I run a code which needs gtest, but terminal shows:
'gtest/gtest.h' file not found
Here is the command:
$ g++ -w -I ../gtest/include/gtest -I../snap-core -I../glib-core -c run-all-tests.cpp
I think I add the path of gtest, but system did not find it.
You need to change
-I ../gtest/include/gtest
to
-I ../gtest/include/
because you are looking for the tile gtest/gtest.h, not gtest/gtest/gtest.h
I'm using a library that generates a whole ton of output to stderr (and there is really no way to suppress the output directly in the code; it is ROOT's Minuit2 minimizer which is known for not having a way to suppress the output). I'm running batch jobs through the LSF system, and the error output files are so big that they exceed my disk quota. Erk.
When I run locally on a shell, I do:
python main.py 2> >( grep -v Minuit2 2>&1 )
to suppress the output, as is done here.
This works great, but unfortunately I can't seem to get that or any variation of it to work when running on LSF. I think this is due to LSF not spawning the necessary subshell, but it's not clear.
I run on batch by passing LSF a submit script. The relevant line is:
python main.py $INPUT_FILE
which works great, aside from the aforementioned problem of gigantic error files.
When I try changing that line to
python main.py $INPUT_FILE 2> >( grep -v Minuit2 2>&1 )
I end up with
./singleSubmit.sh: line 16: syntax error near unexpected token `>'
./singleSubmit.sh: line 16: `python $MAIN $1 2> >( grep -v Minuit2 2>&1 )'
in the error log file.
Any idea how I could accomplish what I want, or why this is not working?
Thanks a ton!
The syntax you're using works in bash, not in csh/tcsh. Try changing the first line of your submission script to
#!/bin/bash