Comments (7)
richelbilderbeek
commented on July 4, 2024
230198@peregrine:scripts Rscript test_is_pff.R
[1] "Run on login node"
[1] "Can create file?"
[1] " "
[1] "filename | can_create_file"
[1] "---|---"
[1] "/local/tmp.txt | FALSE"
[1] "/local/tmp/tmp.txt | TRUE"
[1] "/tmp.txt | FALSE"
[1] "/tmp/tmp.txt | TRUE"
[1] "/data/tmp.txt | FALSE"
[1] "/data/p230198/tmp.txt | TRUE"
[1] "/home/p230198/tmp.txt | TRUE"
[1] "/home/tmp.txt | FALSE"
[1] "Can create BEAST2?"
[1] " "
[1] "prefix | can_run_beast"
[1] "---|---"
[1] "/local | FALSE"
[1] "/local/tmp | TRUE"
[1] "/tmp | FALSE"
[1] "/ | FALSE"
[1] "/data | FALSE"
[1] "/data/p230198 | FALSE"
[1] "/home | FALSE"
[1] "/home/p230198 | FALSE"
There were 14 warnings (use warnings() to see them)
p230198@peregrine:scripts
from peregrine.
richelbilderbeek
commented on July 4, 2024
Rscript test_is_pff.R
[1] "Run on worker node using sbatch"
[1] "Can create file?"
[1] " "
[1] "filename | can_create_file"
[1] "---|---"
[1] "/local/tmp.txt | TRUE"
[1] "/local/tmp/tmp.txt | TRUE"
[1] "/tmp.txt | FALSE"
[1] "/tmp/tmp.txt | TRUE"
[1] "/data/tmp.txt | FALSE"
[1] "/data/p230198/tmp.txt | TRUE"
[1] "/home/p230198/tmp.txt | TRUE"
[1] "/home/tmp.txt | FALSE"
[1] "Can create BEAST2?"
[1] " "
[1] "prefix | can_run_beast"
[1] "---|---"
[1] "/local | TRUE"
[1] "/local/tmp | TRUE"
[1] "/tmp | FALSE"
[1] "/ | FALSE"
[1] "/data | FALSE"
[1] "/data/p230198 | FALSE"
[1] "/home | FALSE"
[1] "/home/p230198 | FALSE"
There were 12 warnings (use warnings() to see them)
###############################################################################
Peregrine Cluster
Job 7273165 for user 'p230198'
Finished at: Mon Aug 12 14:28:16 CEST 2019
Job details:
============
Name : run_r_script
User : p230198
Partition : regular
Nodes : pg-node024
Cores : 1
State : COMPLETED
Submit : 2019-08-12T14:26:59
Start : 2019-08-12T14:27:00
End : 2019-08-12T14:28:16
from peregrine.
richelbilderbeek
commented on July 4, 2024
p230198@peregrine:scripts Rscript test_is_pff.R
[1] "Run on login node"
[1] "Can create file?"
[1] " "
[1] "filename | can_create_file"
[1] "---|---"
[1] "/local/tmp.txt | FALSE"
[1] "/local/tmp/tmp.txt | TRUE"
[1] "/tmp.txt | FALSE"
[1] "/tmp/tmp.txt | TRUE"
[1] "/data/tmp.txt | FALSE"
[1] "/data/p230198/tmp.txt | TRUE"
[1] "/home/p230198/tmp.txt | TRUE"
[1] "/home/tmp.txt | FALSE"
[1] "Can start BEAST2?"
[1] " "
[1] "prefix | can_start_beast"
[1] "---|---"
[1] "/local | FALSE"
[1] "/local/tmp | TRUE"
[1] "/tmp | FALSE"
[1] "/ | FALSE"
[1] "/data | FALSE"
[1] "/data/p230198 | FALSE"
[1] "/home | FALSE"
[1] "/home/p230198 | FALSE"
Warning messages:
1: In file.create(to[okay]) :
cannot create file 'my_file.xml', reason 'Permission denied'
2: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/local/tmp/RtmpefLiIE/beast2_tmp_folder33e26844fd9e/test_output_0.log' to 'out.log', reason 'Invalid cross-device link'
3: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/local/tmp/RtmpefLiIE/beast2_tmp_folder33e26844fd9e/test_output_0.trees' to 'out.trees', reason 'Invalid cross-device link'
4: In file.create(to[okay]) :
cannot create file 'my_file.xml', reason 'Permission denied'
5: In file.create(to[okay]) :
cannot create file 'my_file.xml', reason 'Permission denied'
6: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/local/tmp/RtmpefLiIE/beast2_tmp_folder33e25fd32e8e/test_output_0.log' to 'out.log', reason 'Invalid cross-device link'
7: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/local/tmp/RtmpefLiIE/beast2_tmp_folder33e25fd32e8e/test_output_0.trees' to 'out.trees', reason 'Invalid cross-device link'
8: In file.create(to[okay]) :
cannot create file 'my_file.xml', reason 'Permission denied'
9: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/local/tmp/RtmpefLiIE/beast2_tmp_folder33e27600a033/test_output_0.log' to 'out.log', reason 'Invalid cross-device link'
10: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/local/tmp/RtmpefLiIE/beast2_tmp_folder33e27600a033/test_output_0.trees' to 'out.trees', reason 'Invalid cross-device link'
from peregrine.
richelbilderbeek
commented on July 4, 2024
The following have been reloaded with a version change:
1) Ghostscript/9.23-GCCcore-6.4.0 => Ghostscript/9.22-GCCcore-6.4.0-cairo-1.14.12
2) ImageMagick/6.9.10-5-GCCcore-6.4.0 => ImageMagick/7.0.7-26-foss-2018a
3) LittleCMS/2.9-GCCcore-6.4.0 => LittleCMS/2.9-foss-2018a
4) expat/2.2.5-GCCcore-7.3.0 => expat/2.2.5-GCCcore-6.4.0
Rscript test_is_pff.R
[1] "Run on worker node using sbatch"
[1] "Can create file?"
[1] " "
[1] "filename | can_create_file"
[1] "---|---"
[1] "/local/tmp.txt | TRUE"
[1] "/local/tmp/tmp.txt | TRUE"
[1] "/tmp.txt | FALSE"
[1] "/tmp/tmp.txt | TRUE"
[1] "/data/tmp.txt | FALSE"
[1] "/data/p230198/tmp.txt | TRUE"
[1] "/home/p230198/tmp.txt | TRUE"
[1] "/home/tmp.txt | FALSE"
[1] "Can start BEAST2?"
[1] " "
[1] "prefix | can_start_beast"
[1] "---|---"
[1] "/local | TRUE"
[1] "/local/tmp | TRUE"
[1] "/tmp | FALSE"
[1] "/ | FALSE"
[1] "/data | FALSE"
[1] "/data/p230198 | FALSE"
[1] "/home | FALSE"
[1] "/home/p230198 | FALSE"
Warning messages:
1: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/local/tmp/RtmpRXroWf/beast2_tmp_folder119b6584b5dbf/test_output_0.log' to 'out.log', reason 'Invalid cross-device link'
2: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/local/tmp/RtmpRXroWf/beast2_tmp_folder119b6584b5dbf/test_output_0.trees' to 'out.trees', reason 'Invalid cross-device link'
3: In file.create(to[okay]) :
cannot create file 'my_file.xml', reason 'Permission denied'
4: In file.create(to[okay]) :
cannot create file 'my_file.xml', reason 'Permission denied'
5: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/local/tmp/RtmpRXroWf/beast2_tmp_folder119b625a7a95a/test_output_0.log' to 'out.log', reason 'Invalid cross-device link'
6: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/local/tmp/RtmpRXroWf/beast2_tmp_folder119b625a7a95a/test_output_0.trees' to 'out.trees', reason 'Invalid cross-device link'
7: In file.create(to[okay]) :
cannot create file 'my_file.xml', reason 'Permission denied'
8: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/local/tmp/RtmpRXroWf/beast2_tmp_folder119b67e7516ed/test_output_0.log' to 'out.log', reason 'Invalid cross-device link'
9: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/local/tmp/RtmpRXroWf/beast2_tmp_folder119b67e7516ed/test_output_0.trees' to 'out.trees', reason 'Invalid cross-device link'
###############################################################################
Peregrine Cluster
Job 7273290 for user 'p230198'
Finished at: Mon Aug 12 14:37:58 CEST 2019
Job details:
============
Name : run_r_script
User : p230198
Partition : regular
Nodes : pg-node006
Cores : 1
State : COMPLETED
Submit : 2019-08-12T14:37:13
Start : 2019-08-12T14:37:14
End : 2019-08-12T14:37:58
Reserved walltime :
from peregrine.
richelbilderbeek
commented on July 4, 2024
p230198@peregrine:scripts cat run_r_script_7273290.log
The following have been reloaded with a version change:
1) GCCcore/7.3.0 => GCCcore/6.4.0
2) zlib/1.2.11-GCCcore-7.3.0 => zlib/1.2.11-GCCcore-6.4.0
The following have been reloaded with a version change:
1) Ghostscript/9.23-GCCcore-6.4.0 => Ghostscript/9.22-GCCcore-6.4.0-cairo-1.14.12
2) ImageMagick/6.9.10-5-GCCcore-6.4.0 => ImageMagick/7.0.7-26-foss-2018a
3) LittleCMS/2.9-GCCcore-6.4.0 => LittleCMS/2.9-foss-2018a
4) expat/2.2.5-GCCcore-7.3.0 => expat/2.2.5-GCCcore-6.4.0
Rscript test_is_pff.R
[1] "Run on worker node using sbatch"
[1] "Can create file?"
[1] " "
[1] "filename | can_create_file"
[1] "---|---"
[1] "/local/tmp.txt | TRUE"
[1] "/local/tmp/tmp.txt | TRUE"
[1] "/tmp.txt | FALSE"
[1] "/tmp/tmp.txt | TRUE"
[1] "/data/tmp.txt | FALSE"
[1] "/data/p230198/tmp.txt | TRUE"
[1] "/home/p230198/tmp.txt | TRUE"
[1] "/home/tmp.txt | FALSE"
[1] "Can start BEAST2?"
[1] " "
[1] "prefix | can_start_beast"
[1] "---|---"
[1] "/local | TRUE"
[1] "/local/tmp | TRUE"
[1] "/tmp | FALSE"
[1] "/ | FALSE"
[1] "/data | FALSE"
[1] "/data/p230198 | FALSE"
[1] "/home | FALSE"
[1] "/home/p230198 | FALSE"
Warning messages:
1: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/local/tmp/RtmpRXroWf/beast2_tmp_folder119b6584b5dbf/test_output_0.log' to 'out.log', reason 'Invalid cross-device link'
2: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/local/tmp/RtmpRXroWf/beast2_tmp_folder119b6584b5dbf/test_output_0.trees' to 'out.trees', reason 'Invalid cross-device link'
3: In file.create(to[okay]) :
cannot create file 'my_file.xml', reason 'Permission denied'
4: In file.create(to[okay]) :
cannot create file 'my_file.xml', reason 'Permission denied'
5: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/local/tmp/RtmpRXroWf/beast2_tmp_folder119b625a7a95a/test_output_0.log' to 'out.log', reason 'Invalid cross-device link'
6: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/local/tmp/RtmpRXroWf/beast2_tmp_folder119b625a7a95a/test_output_0.trees' to 'out.trees', reason 'Invalid cross-device link'
7: In file.create(to[okay]) :
cannot create file 'my_file.xml', reason 'Permission denied'
8: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/local/tmp/RtmpRXroWf/beast2_tmp_folder119b67e7516ed/test_output_0.log' to 'out.log', reason 'Invalid cross-device link'
9: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/local/tmp/RtmpRXroWf/beast2_tmp_folder119b67e7516ed/test_output_0.trees' to 'out.trees', reason 'Invalid cross-device link'
###############################################################################
Peregrine Cluster
Job 7273290 for user 'p230198'
Finished at: Mon Aug 12 14:37:58 CEST 2019
Job details:
============
Name : run_r_script
User : p230198
Partition : regular
Nodes : pg-node006
Cores : 1
State : COMPLETED
Submit : 2019-08-12T14:37:13
Start : 2019-08-12T14:37:14
End : 2019-08-12T14:37:58
Reserved walltime : 10:00:00
Used walltime : 00:00:44
Used CPU time : 00:00:42 (efficiency: 96.49%)
% User (Computation): 88.77%
% System (I/O) : 11.23%
Mem reserved : 10G/node
Max Mem used : 174.24M (pg-node006)
Max Disk Write : 133.12K (pg-node006)
Max Disk Read : 3.14M (pg-node006)
from peregrine.
richelbilderbeek
commented on July 4, 2024
p230198@peregrine:scripts cat run_r_script_7397208.log
The following have been reloaded with a version change:
1) GCCcore/7.3.0 => GCCcore/6.4.0
2) zlib/1.2.11-GCCcore-7.3.0 => zlib/1.2.11-GCCcore-6.4.0
The following have been reloaded with a version change:
1) Ghostscript/9.23-GCCcore-6.4.0 => Ghostscript/9.22-GCCcore-6.4.0-cairo-1.14.12
2) ImageMagick/6.9.10-5-GCCcore-6.4.0 => ImageMagick/7.0.7-26-foss-2018a
3) LittleCMS/2.9-GCCcore-6.4.0 => LittleCMS/2.9-foss-2018a
4) expat/2.2.5-GCCcore-7.3.0 => expat/2.2.5-GCCcore-6.4.0
Rscript test_is_pff.R
[1] "Run on worker node using sbatch"
[1] "Can create file?"
[1] " "
[1] "filename | can_create_file"
[1] "---|---"
[1] "/local/tmp.txt | TRUE"
[1] "/local/tmp/tmp.txt | TRUE"
[1] "/tmp.txt | FALSE"
[1] "/tmp/tmp.txt | TRUE"
[1] "/data/tmp.txt | FALSE"
[1] "/data/p230198/tmp.txt | TRUE"
[1] "/home/p230198/tmp.txt | TRUE"
[1] "/home/tmp.txt | FALSE"
[1] "Can start BEAST2?"
[1] " "
[1] "prefix | can_start_beast"
[1] "---|---"
[1] "/local | TRUE"
[1] "/local/tmp | TRUE"
[1] "/tmp | FALSE"
[1] "/ | FALSE"
[1] "/data | FALSE"
[1] "/data/p230198 | FALSE"
[1] "/home | FALSE"
[1] "/home/p230198 | FALSE"
Warning messages:
1: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/local/tmp/RtmpLXezLA/beast2_tmp_folder5d4266eaee13/test_output_0.log' to 'out.log', reason 'Invalid cross-device link'
2: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/local/tmp/RtmpLXezLA/beast2_tmp_folder5d4266eaee13/test_output_0.trees' to 'out.trees', reason 'Invalid cross-device link'
3: In file.create(to[okay]) :
cannot create file 'my_file.xml', reason 'Permission denied'
4: In file.create(to[okay]) :
cannot create file 'my_file.xml', reason 'Permission denied'
5: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/local/tmp/RtmpLXezLA/beast2_tmp_folder5d42a33b5be/test_output_0.log' to 'out.log', reason 'Invalid cross-device link'
6: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/local/tmp/RtmpLXezLA/beast2_tmp_folder5d42a33b5be/test_output_0.trees' to 'out.trees', reason 'Invalid cross-device link'
7: In file.create(to[okay]) :
cannot create file 'my_file.xml', reason 'Permission denied'
8: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/local/tmp/RtmpLXezLA/beast2_tmp_folder5d42542c586f/test_output_0.log' to 'out.log', reason 'Invalid cross-device link'
9: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/local/tmp/RtmpLXezLA/beast2_tmp_folder5d42542c586f/test_output_0.trees' to 'out.trees', reason 'Invalid cross-device link'
[1] "Can use BEAST2?"
[1] "getwd(): /home/p230198"
[1] " "
[1] "folder_name | can_use_beast"
[1] "---|---"
[1] "/tmp | FALSE"
[1] "/local/tmp | TRUE"
[1] "/data/p230198 | FALSE"
[1] "/home/p230198 | TRUE"
Warning messages:
1: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/home/p230198/.cache/file5d427da6066c/test_output_0.log' to '/tmp/out.log', reason 'Invalid cross-device link'
2: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/home/p230198/.cache/file5d427da6066c/test_output_0.trees' to '/tmp/out.trees', reason 'Invalid cross-device link'
3: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/home/p230198/.cache/file5d42b052492/test_output_0.log' to '/local/tmp/out.log', reason 'Invalid cross-device link'
4: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/home/p230198/.cache/file5d42b052492/test_output_0.trees' to '/local/tmp/out.trees', reason 'Invalid cross-device link'
5: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/home/p230198/.cache/file5d4230943ffa/test_output_0.log' to '/data/p230198/out.log', reason 'Invalid cross-device link'
6: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/home/p230198/.cache/file5d4230943ffa/test_output_0.trees' to '/data/p230198/out.trees', reason 'Invalid cross-device link'
[1] "Can use working dir?"
[1] "getwd(): /home/p230198"
[1] " "
[1] "folder_name | can_use_working_dir"
[1] "---|---"
[1] "/tmp | FALSE"
[1] "/local/tmp | FALSE"
[1] "/data/p230198 | FALSE"
[1] "/home/p230198 | TRUE"
Warning messages:
1: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/tmp/test_output_0.log' to '/home/p230198/.cache/file5d4279c804cd/out.log', reason 'Invalid cross-device link'
2: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/tmp/test_output_0.trees' to '/home/p230198/.cache/file5d422d446f4/out.trees', reason 'Invalid cross-device link'
3: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/local/tmp/test_output_0.log' to '/home/p230198/.cache/file5d422284f712/out.log', reason 'Invalid cross-device link'
4: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/local/tmp/test_output_0.trees' to '/home/p230198/.cache/file5d425e04217f/out.trees', reason 'Invalid cross-device link'
5: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/data/p230198/test_output_0.log' to '/home/p230198/.cache/file5d421ba9e4b8/out.log', reason 'Invalid cross-device link'
6: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/data/p230198/test_output_0.trees' to '/home/p230198/.cache/file5d42cffbd48/out.trees', reason 'Invalid cross-device link'
###############################################################################
Peregrine Cluster
Job 7397208 for user 'p230198'
Finished at: Tue Aug 20 08:23:59 CEST 2019
Job details:
============
Name : run_r_script
User : p230198
Partition : regular
Nodes : pg-node007
Cores : 1
State : COMPLETED
Submit : 2019-08-20T08:22:12
Start : 2019-08-20T08:22:13
End : 2019-08-20T08:23:59
Reserved walltime : 10:00:00
Used walltime : 00:01:46
Used CPU time : 00:01:37 (efficiency: 91.63%)
% User (Computation): 90.26%
% System (I/O) : 9.74%
Mem reserved : 10G/node
Max Mem used : 219.58M (pg-node007)
Max Disk Write : 133.12K (pg-node007)
Max Disk Read : 3.14M (pg-node007)
Acknowledgements:
=================
Please see this page if you want to acknowledge Peregrine in your publications:
https://redmine.hpc.rug.nl/redmine/projects/peregrine/wiki/ScientificOutput
################################################################################
from peregrine.
richelbilderbeek
commented on July 4, 2024
Note that /local/tmp can be used to store BEAST2 output file, but cannot be used as a working directory.
from peregrine.
Related Issues (11)
- Use BEAST2 smart HOT 11
- Can use /scratch folder?
- Add video on run_r_cmd HOT 1
- Cannot install R package rstan on Peregrine HOT 2
- Error in if (capabilities("libcurl")) { : argument is of length zero HOT 3
- Peregrine terminal freezes after cp HOT 1
- Put job first in your queue HOT 3
- Test gelifes nodes HOT 2
- Is '/data/...' a Peregrine unfriendly filename? HOT 1
- Can pirouette still run on Peregrine? HOT 4
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from peregrine.