TripalDaemon' does not have a method 'setFilename'

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TripalDaemon' does not have a method 'setFilename'

Sofia Robb
Hi,

When I start the tripaldaemon (drush trpjob-daemon start) I get this error:

Note: The PHP error_log at /var/log/php_errors.log is not writable! Errors will be written to STDERR. Fix the permissions problem or correct the error_log path.
PHP Warning: call_user_func() expects parameter 1 to be a valid callback, class 'TripalDaemon' does not have a method 'setFilename' in /var/www/sites/all/modules/drushd/drushd.drush.inc on line 163 pid 11714

for the first error i have modified the php.ini to change the path, changed the owner and group on the file to apache but no luck.

The second error is the real problem. I checked, I am running drush 6.4.0 and I ran a drush pm-update and TripaDaemon seems to not need an update. Everything is up to date.

What am I missing?


Thank you,
Sofia


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Re: TripalDaemon' does not have a method 'setFilename'

Kucheran, Lacey Sanderson
Hmmm… What version of the PHP Daemon library do you have?
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On November 4, 2015 at 12:18:41 PM, Sofia Robb ([hidden email]) wrote:

Hi,

When I start the tripaldaemon (drush trpjob-daemon start) I get this error:

Note: The PHP error_log at /var/log/php_errors.log is not writable! Errors will be written to STDERR. Fix the permissions problem or correct the error_log path.
PHP Warning: call_user_func() expects parameter 1 to be a valid callback, class 'TripalDaemon' does not have a method 'setFilename' in /var/www/sites/all/modules/drushd/drushd.drush.inc on line 163 pid 11714

for the first error i have modified the php.ini to change the path, changed the owner and group on the file to apache but no luck.

The second error is the real problem. I checked, I am running drush 6.4.0 and I ran a drush pm-update and TripaDaemon seems to not need an update. Everything is up to date.

What am I missing?


Thank you,
Sofia

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Re: TripalDaemon' does not have a method 'setFilename'

Sofia Robb
How can I tell? My Readme looks just like the current one on github.


# PHP Simple Daemon #

Create solid, long-running PHP daemon processes by extending the Core_Daemon class. Use a built-in timer to run your application in second or sub-second frequencies, or build servers using libraries like Socket and LibEvent. Create conventional single-process applications or choose true parallel processing in PHP with persistent background workers.

> Note: For many reasons PHP is not an optimal language choice for creating servers or daemons. I created this library so if you *must* use PHP for these things, you can do it with ease and produce great results. But if you have the choice, Java, Python, Ruby, etc, are all better suited for this.

#### Requires: ###
* PHP 5.3 or Higher
* A POSIX compatible operating system (Linux, OSX, BSD)
* POSIX and PCNTL Extensions for PHP

#### [NEW] Development Plan for v2.2
* Refactor code to use dependency injection and begin writing unit tests.
* Namespace the code
* Investigate updating the minimum version to PHP5.4.

#### Daemon Monitoring
* Over the last few years I've built and deployed many daemons based on this library as well as cron jobs of all sorts. Recently I launched https://cronitor.io -- a dead simple cron (and daemon!) monitoring service. With one line of code you can integrate Cronitor into your daemon and get email/sms alerts if anything goes wrong.

#### [NEW] Version 2.1 Released!
* After a 9 month beta period, the code that was in the branch `feature_abstract_ipc` has been merged into master as v2.1
* Version 2.0 available in the v2.0 tag.
* Exciting features in 2.1 include:
  * A major refactoring of the Worker API includes pluggable IPC classes: Channel worker communication over any popular message queue or stick with the built-in SysV channel.
  * Improved, simpler worker debug shell with new, powerful commands and easier integration of custom breakpoints into your own worker code.
  * Centralize all the process forking, reaping and management code spread around the `Core_Daemon` and `Core_Worker_Mediator` classes into a simple ProcessManager plugin.
  * Dozens of other bug fixes and improvements towards simpler, clearer code in the core Daemon and Mediator classes.

On Wed, Nov 4, 2015 at 11:22 AM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hmmm… What version of the PHP Daemon library do you have?
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On November 4, 2015 at 12:18:41 PM, Sofia Robb ([hidden email]) wrote:

Hi,

When I start the tripaldaemon (drush trpjob-daemon start) I get this error:

Note: The PHP error_log at /var/log/php_errors.log is not writable! Errors will be written to STDERR. Fix the permissions problem or correct the error_log path.
PHP Warning: call_user_func() expects parameter 1 to be a valid callback, class 'TripalDaemon' does not have a method 'setFilename' in /var/www/sites/all/modules/drushd/drushd.drush.inc on line 163 pid 11714

for the first error i have modified the php.ini to change the path, changed the owner and group on the file to apache but no luck.

The second error is the real problem. I checked, I am running drush 6.4.0 and I ran a drush pm-update and TripaDaemon seems to not need an update. Everything is up to date.

What am I missing?


Thank you,
Sofia

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Re: TripalDaemon' does not have a method 'setFilename'

Sofia Robb
Ok, so even though I get the error, I think the tripaldaemon seems to be running fine. Some of my other tripal submitted jobs started without me manually starting them with drush. But I am getting errors with my blast, that look like permission errors, but my /tmp dir is writable by all.

ls -l /
drwxrwxrwt.  21 root root       4096 Nov  6 15:57 tmp

looks like my user, tomcat and root can all write to /tmp

rwxr-xr-x  2 tomcat  tomcat                17 Nov  6 15:30 hsperfdata_tomcat
drwx------  3 root    root                  16 Nov  6 15:30 systemd-private-gi1o5c
drwx------  2 root    root                   6 Nov  6 15:30 vmware-root
-rw-r--r--  1 smr users  219227 Nov  6 15:30 drupal-TripalDaemon_20151106.log
-rw-r--r--  1 smr users     151 Nov  6 15:29 drupal-TripalDaemon.status

Any ideas?

Thanks,
Sofia

Below are my errors when I manually start my blast job:

Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: run_BLAST_tripal_job(blastn, /tmp/2015Nov06_165042_query.fasta, /data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt, 2015Nov06_165042, Array, 137)

Executing blastn

Query: /tmp/2015Nov06_165042_query.fasta
Database: /data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt
Results File: /tmp/2015Nov06_165042.blast.asn
Options:
        evalue: 10
        word_size: 28
        gapopen: 5
        gapextend: 2
        penalty: -2
        reward: 1

Executing the following BLAST command:
blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1
Command line argument error: Argument "query". File is not accessible:  `/tmp/2015Nov06_165042_query.fasta'
WD blast_ui: BLAST did not complete successfully as is implied by the lack of output file                       [error]
(/tmp/2015Nov06_165042.blast.asn). The command run was blastn -query '/tmp/2015Nov06_165042_query.fasta' -db
'/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn'
-outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1
ERROR (BLAST_UI): BLAST did not complete successfully as is implied by the lack of output file (/tmp/2015Nov06_165042.blast.asn). The command run was blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1
[TRIPAL ERROR] ERROR (BLAST_UI): BLAST did not complete successfully as is implied by the lack of output file (/tmp/2015Nov06_165042.blast.asn). The command run was blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1

On Wed, Nov 4, 2015 at 11:56 AM, Sofia Robb <[hidden email]> wrote:
How can I tell? My Readme looks just like the current one on github.


# PHP Simple Daemon #

Create solid, long-running PHP daemon processes by extending the Core_Daemon class. Use a built-in timer to run your application in second or sub-second frequencies, or build servers using libraries like Socket and LibEvent. Create conventional single-process applications or choose true parallel processing in PHP with persistent background workers.

> Note: For many reasons PHP is not an optimal language choice for creating servers or daemons. I created this library so if you *must* use PHP for these things, you can do it with ease and produce great results. But if you have the choice, Java, Python, Ruby, etc, are all better suited for this.

#### Requires: ###
* PHP 5.3 or Higher
* A POSIX compatible operating system (Linux, OSX, BSD)
* POSIX and PCNTL Extensions for PHP

#### [NEW] Development Plan for v2.2
* Refactor code to use dependency injection and begin writing unit tests.
* Namespace the code
* Investigate updating the minimum version to PHP5.4.

#### Daemon Monitoring
* Over the last few years I've built and deployed many daemons based on this library as well as cron jobs of all sorts. Recently I launched https://cronitor.io -- a dead simple cron (and daemon!) monitoring service. With one line of code you can integrate Cronitor into your daemon and get email/sms alerts if anything goes wrong.

#### [NEW] Version 2.1 Released!
* After a 9 month beta period, the code that was in the branch `feature_abstract_ipc` has been merged into master as v2.1
* Version 2.0 available in the v2.0 tag.
* Exciting features in 2.1 include:
  * A major refactoring of the Worker API includes pluggable IPC classes: Channel worker communication over any popular message queue or stick with the built-in SysV channel.
  * Improved, simpler worker debug shell with new, powerful commands and easier integration of custom breakpoints into your own worker code.
  * Centralize all the process forking, reaping and management code spread around the `Core_Daemon` and `Core_Worker_Mediator` classes into a simple ProcessManager plugin.
  * Dozens of other bug fixes and improvements towards simpler, clearer code in the core Daemon and Mediator classes.

On Wed, Nov 4, 2015 at 11:22 AM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hmmm… What version of the PHP Daemon library do you have?
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On November 4, 2015 at 12:18:41 PM, Sofia Robb ([hidden email]) wrote:

Hi,

When I start the tripaldaemon (drush trpjob-daemon start) I get this error:

Note: The PHP error_log at /var/log/php_errors.log is not writable! Errors will be written to STDERR. Fix the permissions problem or correct the error_log path.
PHP Warning: call_user_func() expects parameter 1 to be a valid callback, class 'TripalDaemon' does not have a method 'setFilename' in /var/www/sites/all/modules/drushd/drushd.drush.inc on line 163 pid 11714

for the first error i have modified the php.ini to change the path, changed the owner and group on the file to apache but no luck.

The second error is the real problem. I checked, I am running drush 6.4.0 and I ran a drush pm-update and TripaDaemon seems to not need an update. Everything is up to date.

What am I missing?


Thank you,
Sofia

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Re: TripalDaemon' does not have a method 'setFilename'

Kucheran, Lacey Sanderson
Hi Sofia,

It does look like a permissions error… Can you try running the command manually on the command-line:
blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1

Also, did you check that the query file specified is in your tmp directory? Perhaps it’s an error uploading/creating the file. Did you attach the query file or place it in the text area?

Thanks!
~Lacey
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On November 6, 2015 at 4:06:41 PM, Sofia Robb ([hidden email]) wrote:

Ok, so even though I get the error, I think the tripaldaemon seems to be running fine. Some of my other tripal submitted jobs started without me manually starting them with drush. But I am getting errors with my blast, that look like permission errors, but my /tmp dir is writable by all.

ls -l /
drwxrwxrwt.  21 root root       4096 Nov  6 15:57 tmp

looks like my user, tomcat and root can all write to /tmp

rwxr-xr-x  2 tomcat  tomcat                17 Nov  6 15:30 hsperfdata_tomcat
drwx------  3 root    root                  16 Nov  6 15:30 systemd-private-gi1o5c
drwx------  2 root    root                   6 Nov  6 15:30 vmware-root
-rw-r--r--  1 smr users  219227 Nov  6 15:30 drupal-TripalDaemon_20151106.log
-rw-r--r--  1 smr users     151 Nov  6 15:29 drupal-TripalDaemon.status

Any ideas?

Thanks,
Sofia

Below are my errors when I manually start my blast job:

Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: run_BLAST_tripal_job(blastn, /tmp/2015Nov06_165042_query.fasta, /data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt, 2015Nov06_165042, Array, 137)

Executing blastn

Query: /tmp/2015Nov06_165042_query.fasta
Database: /data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt
Results File: /tmp/2015Nov06_165042.blast.asn
Options:
        evalue: 10
        word_size: 28
        gapopen: 5
        gapextend: 2
        penalty: -2
        reward: 1

Executing the following BLAST command:
blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1
Command line argument error: Argument "query". File is not accessible:  `/tmp/2015Nov06_165042_query.fasta'
WD blast_ui: BLAST did not complete successfully as is implied by the lack of output file                       [error]
(/tmp/2015Nov06_165042.blast.asn). The command run was blastn -query '/tmp/2015Nov06_165042_query.fasta' -db
'/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn'
-outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1
ERROR (BLAST_UI): BLAST did not complete successfully as is implied by the lack of output file (/tmp/2015Nov06_165042.blast.asn). The command run was blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1
[TRIPAL ERROR] ERROR (BLAST_UI): BLAST did not complete successfully as is implied by the lack of output file (/tmp/2015Nov06_165042.blast.asn). The command run was blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1

On Wed, Nov 4, 2015 at 11:56 AM, Sofia Robb <[hidden email]> wrote:
How can I tell? My Readme looks just like the current one on github.


# PHP Simple Daemon #

Create solid, long-running PHP daemon processes by extending the Core_Daemon class. Use a built-in timer to run your application in second or sub-second frequencies, or build servers using libraries like Socket and LibEvent. Create conventional single-process applications or choose true parallel processing in PHP with persistent background workers.

> Note: For many reasons PHP is not an optimal language choice for creating servers or daemons. I created this library so if you *must* use PHP for these things, you can do it with ease and produce great results. But if you have the choice, Java, Python, Ruby, etc, are all better suited for this.

#### Requires: ###
* PHP 5.3 or Higher
* A POSIX compatible operating system (Linux, OSX, BSD)
* POSIX and PCNTL Extensions for PHP

#### [NEW] Development Plan for v2.2
* Refactor code to use dependency injection and begin writing unit tests.
* Namespace the code
* Investigate updating the minimum version to PHP5.4.

#### Daemon Monitoring
* Over the last few years I've built and deployed many daemons based on this library as well as cron jobs of all sorts. Recently I launched https://cronitor.io -- a dead simple cron (and daemon!) monitoring service. With one line of code you can integrate Cronitor into your daemon and get email/sms alerts if anything goes wrong.

#### [NEW] Version 2.1 Released!
* After a 9 month beta period, the code that was in the branch `feature_abstract_ipc` has been merged into master as v2.1
* Version 2.0 available in the v2.0 tag.
* Exciting features in 2.1 include:
  * A major refactoring of the Worker API includes pluggable IPC classes: Channel worker communication over any popular message queue or stick with the built-in SysV channel.
  * Improved, simpler worker debug shell with new, powerful commands and easier integration of custom breakpoints into your own worker code.
  * Centralize all the process forking, reaping and management code spread around the `Core_Daemon` and `Core_Worker_Mediator` classes into a simple ProcessManager plugin.
  * Dozens of other bug fixes and improvements towards simpler, clearer code in the core Daemon and Mediator classes.

On Wed, Nov 4, 2015 at 11:22 AM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hmmm… What version of the PHP Daemon library do you have?
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On November 4, 2015 at 12:18:41 PM, Sofia Robb ([hidden email]) wrote:

Hi,

When I start the tripaldaemon (drush trpjob-daemon start) I get this error:

Note: The PHP error_log at /var/log/php_errors.log is not writable! Errors will be written to STDERR. Fix the permissions problem or correct the error_log path.
PHP Warning: call_user_func() expects parameter 1 to be a valid callback, class 'TripalDaemon' does not have a method 'setFilename' in /var/www/sites/all/modules/drushd/drushd.drush.inc on line 163 pid 11714

for the first error i have modified the php.ini to change the path, changed the owner and group on the file to apache but no luck.

The second error is the real problem. I checked, I am running drush 6.4.0 and I ran a drush pm-update and TripaDaemon seems to not need an update. Everything is up to date.

What am I missing?


Thank you,
Sofia

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Re: TripalDaemon' does not have a method 'setFilename'

Sofia Robb
Hi Lacey,

I just figured it out. My temp files were being written to /tmp/systemd-private-xyz instead of /tmp. My CentOS7 system uses systemd. In my /usr/lib/systemd/system/httpd.service file, I had to change PrivateTmp=true to PrivateTmp=false for my tmp files to write to /tmp. Now it works!!!

Thanks,
Sofia


%] cat /usr/lib/systemd/system/httpd.service
[Unit]
Description=The Apache HTTP Server
After=network.target remote-fs.target nss-lookup.target

[Service]
Type=notify
EnvironmentFile=/etc/sysconfig/httpd
ExecStart=/usr/sbin/httpd $OPTIONS -DFOREGROUND
ExecReload=/usr/sbin/httpd $OPTIONS -k graceful
ExecStop=/bin/kill -WINCH ${MAINPID}
# We want systemd to give httpd some time to finish gracefully, but still want
# it to kill httpd after TimeoutStopSec if something went wrong during the
# graceful stop. Normally, Systemd sends SIGTERM signal right after the
# ExecStop, which would kill httpd. We are sending useless SIGCONT here to give
# httpd time to finish.
KillSignal=SIGCONT
PrivateTmp=false

On Tue, Nov 17, 2015 at 3:58 PM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hi Sofia,

It does look like a permissions error… Can you try running the command manually on the command-line:
blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1

Also, did you check that the query file specified is in your tmp directory? Perhaps it’s an error uploading/creating the file. Did you attach the query file or place it in the text area?

Thanks!
~Lacey
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On November 6, 2015 at 4:06:41 PM, Sofia Robb ([hidden email]) wrote:

Ok, so even though I get the error, I think the tripaldaemon seems to be running fine. Some of my other tripal submitted jobs started without me manually starting them with drush. But I am getting errors with my blast, that look like permission errors, but my /tmp dir is writable by all.

ls -l /
drwxrwxrwt.  21 root root       4096 Nov  6 15:57 tmp

looks like my user, tomcat and root can all write to /tmp

rwxr-xr-x  2 tomcat  tomcat                17 Nov  6 15:30 hsperfdata_tomcat
drwx------  3 root    root                  16 Nov  6 15:30 systemd-private-gi1o5c
drwx------  2 root    root                   6 Nov  6 15:30 vmware-root
-rw-r--r--  1 smr users  219227 Nov  6 15:30 drupal-TripalDaemon_20151106.log
-rw-r--r--  1 smr users     151 Nov  6 15:29 drupal-TripalDaemon.status

Any ideas?

Thanks,
Sofia

Below are my errors when I manually start my blast job:

Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: run_BLAST_tripal_job(blastn, /tmp/2015Nov06_165042_query.fasta, /data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt, 2015Nov06_165042, Array, 137)

Executing blastn

Query: /tmp/2015Nov06_165042_query.fasta
Database: /data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt
Results File: /tmp/2015Nov06_165042.blast.asn
Options:
        evalue: 10
        word_size: 28
        gapopen: 5
        gapextend: 2
        penalty: -2
        reward: 1

Executing the following BLAST command:
blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1
Command line argument error: Argument "query". File is not accessible:  `/tmp/2015Nov06_165042_query.fasta'
WD blast_ui: BLAST did not complete successfully as is implied by the lack of output file                       [error]
(/tmp/2015Nov06_165042.blast.asn). The command run was blastn -query '/tmp/2015Nov06_165042_query.fasta' -db
'/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn'
-outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1
ERROR (BLAST_UI): BLAST did not complete successfully as is implied by the lack of output file (/tmp/2015Nov06_165042.blast.asn). The command run was blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1
[TRIPAL ERROR] ERROR (BLAST_UI): BLAST did not complete successfully as is implied by the lack of output file (/tmp/2015Nov06_165042.blast.asn). The command run was blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1

On Wed, Nov 4, 2015 at 11:56 AM, Sofia Robb <[hidden email]> wrote:
How can I tell? My Readme looks just like the current one on github.


# PHP Simple Daemon #

Create solid, long-running PHP daemon processes by extending the Core_Daemon class. Use a built-in timer to run your application in second or sub-second frequencies, or build servers using libraries like Socket and LibEvent. Create conventional single-process applications or choose true parallel processing in PHP with persistent background workers.

> Note: For many reasons PHP is not an optimal language choice for creating servers or daemons. I created this library so if you *must* use PHP for these things, you can do it with ease and produce great results. But if you have the choice, Java, Python, Ruby, etc, are all better suited for this.

#### Requires: ###
* PHP 5.3 or Higher
* A POSIX compatible operating system (Linux, OSX, BSD)
* POSIX and PCNTL Extensions for PHP

#### [NEW] Development Plan for v2.2
* Refactor code to use dependency injection and begin writing unit tests.
* Namespace the code
* Investigate updating the minimum version to PHP5.4.

#### Daemon Monitoring
* Over the last few years I've built and deployed many daemons based on this library as well as cron jobs of all sorts. Recently I launched https://cronitor.io -- a dead simple cron (and daemon!) monitoring service. With one line of code you can integrate Cronitor into your daemon and get email/sms alerts if anything goes wrong.

#### [NEW] Version 2.1 Released!
* After a 9 month beta period, the code that was in the branch `feature_abstract_ipc` has been merged into master as v2.1
* Version 2.0 available in the v2.0 tag.
* Exciting features in 2.1 include:
  * A major refactoring of the Worker API includes pluggable IPC classes: Channel worker communication over any popular message queue or stick with the built-in SysV channel.
  * Improved, simpler worker debug shell with new, powerful commands and easier integration of custom breakpoints into your own worker code.
  * Centralize all the process forking, reaping and management code spread around the `Core_Daemon` and `Core_Worker_Mediator` classes into a simple ProcessManager plugin.
  * Dozens of other bug fixes and improvements towards simpler, clearer code in the core Daemon and Mediator classes.

On Wed, Nov 4, 2015 at 11:22 AM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hmmm… What version of the PHP Daemon library do you have?
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On November 4, 2015 at 12:18:41 PM, Sofia Robb ([hidden email]) wrote:

Hi,

When I start the tripaldaemon (drush trpjob-daemon start) I get this error:

Note: The PHP error_log at /var/log/php_errors.log is not writable! Errors will be written to STDERR. Fix the permissions problem or correct the error_log path.
PHP Warning: call_user_func() expects parameter 1 to be a valid callback, class 'TripalDaemon' does not have a method 'setFilename' in /var/www/sites/all/modules/drushd/drushd.drush.inc on line 163 pid 11714

for the first error i have modified the php.ini to change the path, changed the owner and group on the file to apache but no luck.

The second error is the real problem. I checked, I am running drush 6.4.0 and I ran a drush pm-update and TripaDaemon seems to not need an update. Everything is up to date.

What am I missing?


Thank you,
Sofia

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Re: TripalDaemon' does not have a method 'setFilename'

Stephen Ficklin-2
HI Sofia,

Is there any text you might recommend to be added to our CentOS7 page that could help future folks from hitting on this same problem:

http://tripal.info/node/150

Thanks,
Stephen

On 11/17/2015 3:18 PM, Sofia Robb wrote:
Hi Lacey,

I just figured it out. My temp files were being written to /tmp/systemd-private-xyz instead of /tmp. My CentOS7 system uses systemd. In my /usr/lib/systemd/system/httpd.service file, I had to change PrivateTmp=true to PrivateTmp=false for my tmp files to write to /tmp. Now it works!!!

Thanks,
Sofia


%] cat /usr/lib/systemd/system/httpd.service
[Unit]
Description=The Apache HTTP Server
After=network.target remote-fs.target nss-lookup.target

[Service]
Type=notify
EnvironmentFile=/etc/sysconfig/httpd
ExecStart=/usr/sbin/httpd $OPTIONS -DFOREGROUND
ExecReload=/usr/sbin/httpd $OPTIONS -k graceful
ExecStop=/bin/kill -WINCH ${MAINPID}
# We want systemd to give httpd some time to finish gracefully, but still want
# it to kill httpd after TimeoutStopSec if something went wrong during the
# graceful stop. Normally, Systemd sends SIGTERM signal right after the
# ExecStop, which would kill httpd. We are sending useless SIGCONT here to give
# httpd time to finish.
KillSignal=SIGCONT
PrivateTmp=false

On Tue, Nov 17, 2015 at 3:58 PM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hi Sofia,

It does look like a permissions error… Can you try running the command manually on the command-line:
blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1

Also, did you check that the query file specified is in your tmp directory? Perhaps it’s an error uploading/creating the file. Did you attach the query file or place it in the text area?

Thanks!
~Lacey
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a moz-do-not-send="true" href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On November 6, 2015 at 4:06:41 PM, Sofia Robb ([hidden email]) wrote:

Ok, so even though I get the error, I think the tripaldaemon seems to be running fine. Some of my other tripal submitted jobs started without me manually starting them with drush. But I am getting errors with my blast, that look like permission errors, but my /tmp dir is writable by all.

ls -l /
drwxrwxrwt.  21 root root       4096 Nov  6 15:57 tmp

looks like my user, tomcat and root can all write to /tmp

rwxr-xr-x  2 tomcat  tomcat                17 Nov  6 15:30 hsperfdata_tomcat
drwx------  3 root    root                  16 Nov  6 15:30 systemd-private-gi1o5c
drwx------  2 root    root                   6 Nov  6 15:30 vmware-root
-rw-r--r--  1 smr users  219227 Nov  6 15:30 drupal-TripalDaemon_20151106.log
-rw-r--r--  1 smr users     151 Nov  6 15:29 drupal-TripalDaemon.status

Any ideas?

Thanks,
Sofia

Below are my errors when I manually start my blast job:

Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: run_BLAST_tripal_job(blastn, /tmp/2015Nov06_165042_query.fasta, /data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt, 2015Nov06_165042, Array, 137)

Executing blastn

Query: /tmp/2015Nov06_165042_query.fasta
Database: /data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt
Results File: /tmp/2015Nov06_165042.blast.asn
Options:
        evalue: 10
        word_size: 28
        gapopen: 5
        gapextend: 2
        penalty: -2
        reward: 1

Executing the following BLAST command:
blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1
Command line argument error: Argument "query". File is not accessible:  `/tmp/2015Nov06_165042_query.fasta'
WD blast_ui: BLAST did not complete successfully as is implied by the lack of output file                       [error]
(/tmp/2015Nov06_165042.blast.asn). The command run was blastn -query '/tmp/2015Nov06_165042_query.fasta' -db
'/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn'
-outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1
ERROR (BLAST_UI): BLAST did not complete successfully as is implied by the lack of output file (/tmp/2015Nov06_165042.blast.asn). The command run was blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1
[TRIPAL ERROR] ERROR (BLAST_UI): BLAST did not complete successfully as is implied by the lack of output file (/tmp/2015Nov06_165042.blast.asn). The command run was blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1

On Wed, Nov 4, 2015 at 11:56 AM, Sofia Robb <[hidden email]> wrote:
How can I tell? My Readme looks just like the current one on github.


# PHP Simple Daemon #

Create solid, long-running PHP daemon processes by extending the Core_Daemon class. Use a built-in timer to run your application in second or sub-second frequencies, or build servers using libraries like Socket and LibEvent. Create conventional single-process applications or choose true parallel processing in PHP with persistent background workers.

> Note: For many reasons PHP is not an optimal language choice for creating servers or daemons. I created this library so if you *must* use PHP for these things, you can do it with ease and produce great results. But if you have the choice, Java, Python, Ruby, etc, are all better suited for this.

#### Requires: ###
* PHP 5.3 or Higher
* A POSIX compatible operating system (Linux, OSX, BSD)
* POSIX and PCNTL Extensions for PHP

#### [NEW] Development Plan for v2.2
* Refactor code to use dependency injection and begin writing unit tests.
* Namespace the code
* Investigate updating the minimum version to PHP5.4.

#### Daemon Monitoring
* Over the last few years I've built and deployed many daemons based on this library as well as cron jobs of all sorts. Recently I launched https://cronitor.io -- a dead simple cron (and daemon!) monitoring service. With one line of code you can integrate Cronitor into your daemon and get email/sms alerts if anything goes wrong.

#### [NEW] Version 2.1 Released!
* After a 9 month beta period, the code that was in the branch `feature_abstract_ipc` has been merged into master as v2.1
* Version 2.0 available in the v2.0 tag.
* Exciting features in 2.1 include:
  * A major refactoring of the Worker API includes pluggable IPC classes: Channel worker communication over any popular message queue or stick with the built-in SysV channel.
  * Improved, simpler worker debug shell with new, powerful commands and easier integration of custom breakpoints into your own worker code.
  * Centralize all the process forking, reaping and management code spread around the `Core_Daemon` and `Core_Worker_Mediator` classes into a simple ProcessManager plugin.
  * Dozens of other bug fixes and improvements towards simpler, clearer code in the core Daemon and Mediator classes.

On Wed, Nov 4, 2015 at 11:22 AM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hmmm… What version of the PHP Daemon library do you have?
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a moz-do-not-send="true" href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On November 4, 2015 at 12:18:41 PM, Sofia Robb ([hidden email]) wrote:

Hi,

When I start the tripaldaemon (drush trpjob-daemon start) I get this error:

Note: The PHP error_log at /var/log/php_errors.log is not writable! Errors will be written to STDERR. Fix the permissions problem or correct the error_log path.
PHP Warning: call_user_func() expects parameter 1 to be a valid callback, class 'TripalDaemon' does not have a method 'setFilename' in /var/www/sites/all/modules/drushd/drushd.drush.inc on line 163 pid 11714

for the first error i have modified the php.ini to change the path, changed the owner and group on the file to apache but no luck.

The second error is the real problem. I checked, I am running drush 6.4.0 and I ran a drush pm-update and TripaDaemon seems to not need an update. Everything is up to date.

What am I missing?


Thank you,
Sofia

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------------------------------------------------------------------------------
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Use one codebase in this all-in-one HTML5 development environment.
Design, debug & build mobile apps & 2-D/3-D games for multiple OSs.
Then get your creation into app stores sooner, with many ways to monetize.
http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140


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------------------------------------------------------------------------------
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Use one codebase in this all-in-one HTML5 development environment.
Design, debug & build mobile apps & 2-D/3-D games for multiple OSs.
Then get your creation into app stores sooner, with many ways to monetize.
http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
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Re: TripalDaemon' does not have a method 'setFilename'

Sofia Robb
How about something like this:


If you are executing your blast jobs, manually with drush and you receive an error that is similar to the error below:

Executing the following BLAST command:
blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1
Command line argument error: Argument "query". File is not accessible:  `/tmp/2015Nov06_165042_query.fasta'
WD blast_ui: BLAST did not complete successfully as is implied by the lack of output file                       [error]

First find where your blast temp files are being written (use your own query.fasta file name):

find / -name "2015Nov06_165042_query.fasta"

If you see they ARE being written, but in a directory that has a prefix of systemd-private, you are likely running systemd and need to make a change to your systemd httpd.service file ( /usr/lib/systemd/system/httpd.service ). Change PrivateTmp=true to PrivateTmp=false and restart apache. 

This should solve the problem.

On Tue, Nov 17, 2015 at 4:25 PM, Stephen Ficklin <[hidden email]> wrote:
HI Sofia,

Is there any text you might recommend to be added to our CentOS7 page that could help future folks from hitting on this same problem:

http://tripal.info/node/150

Thanks,
Stephen


On 11/17/2015 3:18 PM, Sofia Robb wrote:
Hi Lacey,

I just figured it out. My temp files were being written to /tmp/systemd-private-xyz instead of /tmp. My CentOS7 system uses systemd. In my /usr/lib/systemd/system/httpd.service file, I had to change PrivateTmp=true to PrivateTmp=false for my tmp files to write to /tmp. Now it works!!!

Thanks,
Sofia


%] cat /usr/lib/systemd/system/httpd.service
[Unit]
Description=The Apache HTTP Server
After=network.target remote-fs.target nss-lookup.target

[Service]
Type=notify
EnvironmentFile=/etc/sysconfig/httpd
ExecStart=/usr/sbin/httpd $OPTIONS -DFOREGROUND
ExecReload=/usr/sbin/httpd $OPTIONS -k graceful
ExecStop=/bin/kill -WINCH ${MAINPID}
# We want systemd to give httpd some time to finish gracefully, but still want
# it to kill httpd after TimeoutStopSec if something went wrong during the
# graceful stop. Normally, Systemd sends SIGTERM signal right after the
# ExecStop, which would kill httpd. We are sending useless SIGCONT here to give
# httpd time to finish.
KillSignal=SIGCONT
PrivateTmp=false

On Tue, Nov 17, 2015 at 3:58 PM, Kucheran, Lacey Sanderson <[hidden email][hidden email]> wrote:
Hi Sofia,

It does look like a permissions error… Can you try running the command manually on the command-line:
blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1

Also, did you check that the query file specified is in your tmp directory? Perhaps it’s an error uploading/creating the file. Did you attach the query file or place it in the text area?

Thanks!
~Lacey
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On November 6, 2015 at 4:06:41 PM, Sofia Robb ([hidden email][hidden email]) wrote:

Ok, so even though I get the error, I think the tripaldaemon seems to be running fine. Some of my other tripal submitted jobs started without me manually starting them with drush. But I am getting errors with my blast, that look like permission errors, but my /tmp dir is writable by all.

ls -l /
drwxrwxrwt.  21 root root       4096 Nov  6 15:57 tmp

looks like my user, tomcat and root can all write to /tmp

rwxr-xr-x  2 tomcat  tomcat                17 Nov  6 15:30 hsperfdata_tomcat
drwx------  3 root    root                  16 Nov  6 15:30 systemd-private-gi1o5c
drwx------  2 root    root                   6 Nov  6 15:30 vmware-root
-rw-r--r--  1 smr users  219227 Nov  6 15:30 drupal-TripalDaemon_20151106.log
-rw-r--r--  1 smr users     151 Nov  6 15:29 drupal-TripalDaemon.status

Any ideas?

Thanks,
Sofia

Below are my errors when I manually start my blast job:

Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: run_BLAST_tripal_job(blastn, /tmp/2015Nov06_165042_query.fasta, /data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt, 2015Nov06_165042, Array, 137)

Executing blastn

Query: /tmp/2015Nov06_165042_query.fasta
Database: /data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt
Results File: /tmp/2015Nov06_165042.blast.asn
Options:
        evalue: 10
        word_size: 28
        gapopen: 5
        gapextend: 2
        penalty: -2
        reward: 1

Executing the following BLAST command:
blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1
Command line argument error: Argument "query". File is not accessible:  `/tmp/2015Nov06_165042_query.fasta'
WD blast_ui: BLAST did not complete successfully as is implied by the lack of output file                       [error]
(/tmp/2015Nov06_165042.blast.asn). The command run was blastn -query '/tmp/2015Nov06_165042_query.fasta' -db
'/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn'
-outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1
ERROR (BLAST_UI): BLAST did not complete successfully as is implied by the lack of output file (/tmp/2015Nov06_165042.blast.asn). The command run was blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1
[TRIPAL ERROR] ERROR (BLAST_UI): BLAST did not complete successfully as is implied by the lack of output file (/tmp/2015Nov06_165042.blast.asn). The command run was blastn -query '/tmp/2015Nov06_165042_query.fasta' -db '/data/organisms/planaria/Smed/SmedSxl/genome/v31/SmedSxl_genome_v3.1.nt' -out '/tmp/2015Nov06_165042.blast.asn' -outfmt=11 -evalue 10 -word_size 28 -gapopen 5 -gapextend 2 -penalty -2 -reward 1

On Wed, Nov 4, 2015 at 11:56 AM, Sofia Robb <[hidden email]> wrote:
How can I tell? My Readme looks just like the current one on github.


# PHP Simple Daemon #

Create solid, long-running PHP daemon processes by extending the Core_Daemon class. Use a built-in timer to run your application in second or sub-second frequencies, or build servers using libraries like Socket and LibEvent. Create conventional single-process applications or choose true parallel processing in PHP with persistent background workers.

> Note: For many reasons PHP is not an optimal language choice for creating servers or daemons. I created this library so if you *must* use PHP for these things, you can do it with ease and produce great results. But if you have the choice, Java, Python, Ruby, etc, are all better suited for this.

#### Requires: ###
* PHP 5.3 or Higher
* A POSIX compatible operating system (Linux, OSX, BSD)
* POSIX and PCNTL Extensions for PHP

#### [NEW] Development Plan for v2.2
* Refactor code to use dependency injection and begin writing unit tests.
* Namespace the code
* Investigate updating the minimum version to PHP5.4.

#### Daemon Monitoring
* Over the last few years I've built and deployed many daemons based on this library as well as cron jobs of all sorts. Recently I launched https://cronitor.io -- a dead simple cron (and daemon!) monitoring service. With one line of code you can integrate Cronitor into your daemon and get email/sms alerts if anything goes wrong.

#### [NEW] Version 2.1 Released!
* After a 9 month beta period, the code that was in the branch `feature_abstract_ipc` has been merged into master as v2.1
* Version 2.0 available in the v2.0 tag.
* Exciting features in 2.1 include:
  * A major refactoring of the Worker API includes pluggable IPC classes: Channel worker communication over any popular message queue or stick with the built-in SysV channel.
  * Improved, simpler worker debug shell with new, powerful commands and easier integration of custom breakpoints into your own worker code.
  * Centralize all the process forking, reaping and management code spread around the `Core_Daemon` and `Core_Worker_Mediator` classes into a simple ProcessManager plugin.
  * Dozens of other bug fixes and improvements towards simpler, clearer code in the core Daemon and Mediator classes.

On Wed, Nov 4, 2015 at 11:22 AM, Kucheran, Lacey Sanderson <[hidden email][hidden email]> wrote:
Hmmm… What version of the PHP Daemon library do you have?
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On November 4, 2015 at 12:18:41 PM, Sofia Robb ([hidden email][hidden email]) wrote:

Hi,

When I start the tripaldaemon (drush trpjob-daemon start) I get this error:

Note: The PHP error_log at /var/log/php_errors.log is not writable! Errors will be written to STDERR. Fix the permissions problem or correct the error_log path.
PHP Warning: call_user_func() expects parameter 1 to be a valid callback, class 'TripalDaemon' does not have a method 'setFilename' in /var/www/sites/all/modules/drushd/drushd.drush.inc on line 163 pid 11714

for the first error i have modified the php.ini to change the path, changed the owner and group on the file to apache but no luck.

The second error is the real problem. I checked, I am running drush 6.4.0 and I ran a drush pm-update and TripaDaemon seems to not need an update. Everything is up to date.

What am I missing?


Thank you,
Sofia

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