Closed richelbilderbeek closed 2 years ago
FATAL: could not open image /home/richel/nsphs_ml_qt.sif: failed to retrieve path for /home/richel/nsphs_ml_qt.sif: lstat /castor/project/home/richel/nsphs_ml_qt.sif: no such file or directory
I guess the path expansion is the problem:
[richel@sens2021565-bianca ~]$ cat data_issue_5/experiment_params.csv
parameter,value
datadir,/home/richel/data_issue_5/
data,data_issue_5
superpops,/home/richel/data_issue_5/data_issue_5_labels.csv
model_id,M1
train_opts_id,ex3
data_opts_id,b_0_4
trainedmodeldir,~/data_issue_5_ae/
pheno_model_id,p0
analyse_epochs,"10,20,30,40,50,60,70,80,90,100,110,120,130,140,150,160,170,180,190,200,210,220,230,240,250,260,270,280,290,300,310,320,330,340,350,360,370,380,390,400,410,420,430,440,450,460,470,480,490,500,510,520,530,540,550,560,570,580,590,600,610,620,630,640,650,660,670,680,690,700,710,720,730,740,750,760,770,780,790,800,810,820,830,840,850,860,870,880,890,900,910,920,930,940,950,960,970,980,990,1000"
metrics,"f1_score_3,f1_score_5,f1_score_7,f1_score_9,f1_score_11"
gcae_folder,/opt/gcae_richel
ormr_folder_name,python3
gcae_version,1.0
python_version,3.6
That was a step in the right direction. Still, the _ae
folder does not exist. Is it really needed already?
Error in gcae_train_more(gcae_setup = gcae_experiment_params$gcae_setup, :
'ae_out_subfolder' not found at path '/home/richel/data_issue_5_ae/ae.M1.ex3.b_0_4.data_issue_5.p0'
'gcae_options$gcae_folder': /opt/gcae_richel
'gcae_options$ormr_folder_name': python3
'gcae_options$gcae_folder': /opt/gcae_richel
'gcae_options$python_version': 3.6'args': 'train --datadir /home/richel/data_issue_5/ --data data_issue_5 --model_id M1 --resume_from 0 --epochs 10 --save_interval 10 --train_opts_id ex3 --data_opts_id b_0_4 --trainedmodeldir /home/richel/data_issue_5_ae/ --pheno_model_id p0'
Tip: you should be able to copy-paste the args :-)
Calls: <Anonymous> -> gcae_train_more
In addition: Warning message:
In system2(command = run_args[1], args = run_args[-1], stdout = TRUE, :
running command ''python3' /opt/gcae_richel/run_gcae.py train --datadir /home/richel/data_issue_5/ --data data_issue_5 --model_id M1 --resume_from 0 --epochs 10 --save_interval 10 --train_opts_id ex3 --data_opts_id b_0_4 --trainedmodeldir /home/richel/data_issue_5_ae/ --pheno_model_id p0 2>&1' had status 1
Execution halted
Hmmm, locally gcaer
does create the output folder, even if it is a sub-sub-sub folder:
gcae_options <- create_gcae_options()
gcae_setup <- create_gcae_setup(
datadir = get_test_datadir(),
data = "gcae_input_files_1",
superpops = get_gcaer_filename("gcae_input_files_1_labels.csv"),
model_id = "M1",
data_opts_id = "b_0_4",
train_opts_id = "ex3",
pheno_model_id = "p2",
trainedmodeldir = paste0(
normalizePath(
file.path(get_gcaer_tempfilename(), "sub", "sub", "gcae_input_files_1_ae"),
mustWork = FALSE
), "/"
)
)
# 2. Train, approx 3 mins
Sys.time()
train_filenames <- gcae_train_more(
gcae_setup = gcae_setup,
resume_from = 0,
epochs = 1,
save_interval = 1,
verbose = TRUE
)
with last lines of GCAE output:
-------- Save time: 0.015036 dir: /home/richel/.cache/gcaer/file43ad347905ae/sub/sub/gcae_input_files_1_ae/ae.M1.ex3.b_0_4.gcae_input_files_1.p2/weights/1
Done training. Wrote to /home/richel/.cache/gcaer/file43ad347905ae/sub/sub/gcae_input_files_1_ae/ae.M1.ex3.b_0_4.gcae_input_files_1.p2
It is there and it works :-)
Now Sylabs has given me more space, I can use it with a new container :-)