Comments (4)
This one works:
p230198@peregrine:peregrine cat scripts/run_pir.R
# R script to test if pirouette runs on peregrine
pirouette::pir_run(
phylogeny = ape::read.tree(text = "((A:2, B:2):1, C:3);"),
pir_params = peregrine::create_test_pff_pir_params()
)
p230198@peregrine:peregrine sbatch scripts/run_r_script scripts/run_pir.R
Submitted batch job 7443244
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
7443244 regular run_r_sc p230198 CG 0:16 1 pg-node027
p230198@peregrine:peregrine cat *.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 scripts/run_pir.R
Registered S3 method overwritten by 'geiger':
method from
unique.multiPhylo ape
tree inference_model inference_model_weight site_model clock_model tree_prior
1 true generative NA JC69 strict yule
error_1 error_2 error_3
1 0.04450728 0.19498 0.1912832
###############################################################################
Peregrine Cluster
Job 7443244 for user 'p230198'
Finished at: Tue Aug 27 12:23:58 CEST 2019
Job details:
============
Name : run_r_script
User : p230198
Partition : regular
Nodes : pg-node027
Cores : 1
State : COMPLETED
Submit : 2019-08-27T12:23:42
Start : 2019-08-27T12:23:42
End : 2019-08-27T12:23:58
Reserved walltime : 10:00:00
Used walltime : 00:00:16
Used CPU time : 00:00:11 (efficiency: 74.70%)
% User (Computation): 87.02%
% System (I/O) : 12.97%
Mem reserved : 10G/node
Max Mem used : 0.00 (pg-node027)
Max Disk Write : 0.00 (pg-node027)
Max Disk Read : 0.00 (pg-node027)
from peregrine.
Gotcha!
p230198@peregrine:peregrine sbatch scripts/run_r_script scripts/run_pir.R
Submitted batch job 7443269
p230198@peregrine:peregrine q
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
7443269 regular run_r_sc p230198 R 0:11 1 pg-node009
p230198@peregrine:peregrine cat run_r_script_7443269.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 scripts/run_pir.R
Registered S3 method overwritten by 'geiger':
method from
unique.multiPhylo ape
Error in value[[3L]](cond) : Could not estimate the marginal likelihood.
Error message: File 'output_log_filename' not found. Could not find file with path '/local/tmp/Rtmpoc5Ir4/file17ada2d07488.log'
site_model$name: GTR
clock_model$name: relaxed_log_normal
tree_prior$name: birth_death
epsilon: 1e-12
rng_seed: NA
verbose: FALSE
beast2_working_dir: /home/p230198/.cache/file17ada73b9da98/beast2_tmp_folder17ada5721a71f
beast2_bin_path: /home/p230198/.local/share/beast/bin/beast
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
In addition: Warning messages:
1: In file.rename(from = actual_log_filename, to = output_log_filename) :
cannot rename file '/home/p230198/.cache/file17ada73b9da98/beast2_tmp_folder17ada5721a71f/pff_17adac1a0d9b_evidence.log' to '/local/tmp/Rtmpoc5Ir4/file17ada2d07488.log', reason 'Invalid cross-device link'
2: In file.rename(from = actual_trees_filename, to = to) :
cannot rename file '/home/p230198/.cache/file17ada73b9da98/beast2_tmp_folder17ada5721a71f/pff_17adac1a0d9b_evidence.trees' to '/local/tmp/Rtmpoc5Ir4/file17ada7c47b2c2.trees', reason 'Invalid cross-device link'
Execution halted
###############################################################################
Peregrine Cluster
Job 7443269 for user 'p230198'
Finished at: Tue Aug 27 12:35:23 CEST 2019
Job details:
============
Name : run_r_script
User : p230198
Partition : regular
Nodes : pg-node009
Cores : 1
State : FAILED
Submit : 2019-08-27T12:34:37
Start : 2019-08-27T12:34:38
End : 2019-08-27T12:35:23
Reserved walltime : 10:00:00
Used walltime : 00:00:45
Used CPU time : 00:00:41 (efficiency: 93.16%)
% User (Computation): 92.83%
% System (I/O) : 7.17%
Mem reserved : 10G/node
Max Mem used : 330.92M (pg-node009)
Max Disk Write : 133.12K (pg-node009)
Max Disk Read : 3.14M (pg-node009)
from peregrine.
The error is in the model comparison, check upstream at mcbette Issue 12
from peregrine.
Bug was in mcbette, fixed with mcbette v1.6.
from peregrine.
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from peregrine.