-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathpbs.py
486 lines (404 loc) · 22.1 KB
/
pbs.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
#pbs.py
SSH_TIMEOUT=15
try:
import drmaa
DRMAA_avail = True
except ModuleNotFoundError:
print('No DRMAA, not a submit host')
DRMAA_avail = False
import datetime
import streamlit as st
from subprocess import run, TimeoutExpired
import os,socket
import inet
import tempfile
from common import show_info, check_select, copy_button
from shell import run_cluster_cmd
from sidebar import DEFAULT_WALLTIME
PBS_HOSTS = ['login1', 'login2', 'globus.chpc.ac.za']
host = socket.gethostname()
PBS_HOST=host in PBS_HOSTS
User_RPs = []
def show_pbs(st, pbs_tab):
PBS_dict = {
'bash': '#!/bin/bash', 'programme': 'P',
'email': 'M', 'jobname': 'N', 'queue': 'q',
'error': 'e', 'out': 'o', 'join': 'j oe',
'Interactive' : 'I', 'Xfwd': 'X', 'Vars': 'V',}
dl_file_contents=''
@st.cache_data(persist="disk")
def get_rp_detail(pgms):
prm = '|'.join(pgms)
cmd = "cat /home/userdb/projects_status.csv | grep -E \'" + prm + "\'"
if not DRMAA_avail:
cmd = "ssh " + st.session_state.user + '@' + st.session_state.server + ' ' +cmd
op = run(cmd, capture_output=True, shell=True, timeout=SSH_TIMEOUT, check=True)
if op.stdout is not None:
lines = op.stdout.decode().splitlines()
rp_list=[]
rp_list += [ l.split(',') for l in lines]
pgm_dict = {}
for line in rp_list:
for pgm in pgms:
if pgm == line[0]:
pgm_dict[pgm] = {'start': line[1], 'end': line[2],
'alloc': line[3], 'cpuh': line[4]}
return pgm_dict
#To do: convert above to form # >>> {k:row[0] for row in groups for k in row[1:]}
@st.cache_data(persist="disk")
def get_rp_list(): # get list of matching programmes for user
# op=run_cluster_cmd(st.session_state.user + '@' + st.session_state.server,
# {'rp': 'grep ' + st.session_state.user + ' /home/userdb/programme_info.csv'},'rp','') # fake cmd dict
cmd = 'grep ' + st.session_state.user.rstrip() + ' /home/userdb/programme_info.csv'
if not DRMAA_avail:
cmd = 'ssh ' + st.session_state.user + '@' + st.session_state.server + ' ' + cmd
# else:
# op = run( 'grep ' + st.session_state.user + ' /home/userdb/programme_info.csv',
# import pdb; pdb.set_trace()
op = run(cmd, capture_output=True, shell=True, timeout=SSH_TIMEOUT, check=True)
pgms = []
opl = op.stdout.decode().splitlines()
for line in range(len(opl)):
word = opl[line].split(',')[0]
pgms.append(word)
user_rps=get_rp_detail(pgms)
return user_rps
def show_rp_info(rp_dict, place):
def show_rp_data():
with place.container():
stt = datetime.datetime.strptime(
rp_dict[st.session_state.user_rp]['start'], '%Y%m%d' )
st_d = stt.strftime('%-d %b %Y')
st.info("Start: " + st_d)
et = datetime.datetime.strptime(
rp_dict[st.session_state.user_rp]['end'], '%Y%m%d' )
et_d = et.strftime('%-d %b %Y')
st.info('End: ' + et_d )
st.info('CPU-h : ' + rp_dict[st.session_state.user_rp]['cpuh'] +
' of ' + rp_dict[st.session_state.user_rp]['alloc'])
if et < datetime.datetime.now():
st.write('Expired :warning:')
if 'user_rp' in st.session_state.keys():
show_rp_data()
def copy_pbs_file(file):
filename='/tmp/' + file
fp = open(filename, 'r')
dl_file_contents=fp.read(); fp.close()
#creds = st.session_state.user + '@' + st.session_state.server
st.info("Copying job file to " + st.session_state.workdir)
CMD = 'cp ' + filename + ' ' + "${HOME}/" + st.session_state.workdir + '/'
print("DEBUG copy :", CMD)
exitcode = run(CMD, capture_output=True, shell=True)
if exitcode.returncode < 0:
st.error("Could not copy file to workdir, timeout " + filename + exitcode.returncode)
else:
st.info('File ' + filename + ' copied to workdir ' + \
st.session_state.workdir + '/' + file)
print("DEBUG : " , exitcode.stdout.decode())
st.info(exitcode.stdout.decode())
def send_pbs_file(file):
filename='/tmp/' + file
fp = open(filename, 'r')
dl_file_contents=fp.read(); fp.close()
creds = st.session_state.user + '@' + st.session_state.server
st.info("Copying job file via scp to " + st.session_state.server)
CMD = 'scp ' + filename + ' ' + creds + ':' + st.session_state.workdir
exitcode = run(CMD, capture_output=True, shell=True)
if exitcode.returncode < 0:
st.error("Could not copy file to server, timeout " + filename + exitcode.returncode)
else:
st.info('File ' + filename + ' copied to cluster ' + \
st.session_state.workdir + '/' + file)
def submit_pbs_file(file):
creds = st.session_state.user + '@' + st.session_state.server
if not DRMAA_avail:
qsub_out = run("ssh " + creds + \
' qsub ' + st.session_state.workdir \
+ '/' + file,
capture_output=True, shell=True)
else:
qsub_out = run( \
' qsub ' + "${HOME}/" + st.session_state.workdir \
+ '/' + file,
capture_output=True, shell=True)
if qsub_out.returncode < 0:
st.error("Timeout, Could not run qsub " + qsub_out.returncode)
print("ERROR: Timeout, qsub command failed to send")
return
else:
print("INFO: qsub command sent :", ' qsub ' +
st.session_state.workdir \
+ '/' + file )
st.info('qsub command sent')
if qsub_out.returncode == 0:
jobid = qsub_out.stdout.decode()
st.success('Job ' + str(jobid) + 'submitted')
print("INFO: post qsub ", qsub_out.stdout.decode())
def save_dl_file(cmd):
dl_file_contents=''
for k in cmd.keys():
dl_file_contents += cmd[k] + '\n'
#fname='/tmp/' + st.session_state.jobname + '.pbs'
with tempfile.NamedTemporaryFile(mode='w', delete=False) as fp:
fp.write(dl_file_contents);
#fp.close()
#st.info('File saved to ' + fname )
def read_form():
cmd={};qs_cmd={}
checked=check_select()
for k in PBS_dict:
if k in st.session_state.keys():
if k=='bash':
if st.session_state[k]:
cmd[k] = PBS_dict[k]
elif k in ['jobname', 'email', 'programme']:
if st.session_state[k]:
qs_cmd[k] = '-' + PBS_dict[k] + ' ' + st.session_state[k]
cmd[k] = '#PBS ' + qs_cmd[k]
if k=='email':
qs_cmd['email_opts'] = '-m' + st.session_state.email_opts
cmd['email_opts'] = '#PBS -m ' + st.session_state.email_opts
elif k in [ 'join' , 'interactive', 'Xfwd',]:
if st.session_state[k]:
qs_cmd[k] = '-' + PBS_dict[k]
cmd[k] = '#PBS ' + qs_cmd[k]
else:
if st.session_state[k]:
if k=='queue':
qs_cmd[k] = '-' + PBS_dict[k] + ' ' + checked[k]
cmd[k] = '#PBS ' + qs_cmd[k]
if checked['ngpus']:
selstr = '-l select={}:ncpus={}:mpiprocs={}:ngpus:{}:mem={}GB -l walltime={} '.format(
checked['nodect'], checked['ncpus'], checked['mpiprocs'],
checked['ngpus'], checked['mem'], checked['walltime'],)
else:
selstr = '-l select={}:ncpus={}:mpiprocs={}:mem={}GB -l walltime={} '.format(
checked['nodect'], checked['ncpus'], checked['mpiprocs'], checked['mem'],
checked['walltime'],)
qs_cmd['Select'] = selstr
cmd['Select'] = '#PBS ' + selstr
cmd['modules'] = st.session_state.modules
cmd['command'] = st.session_state.command
qs_cmd['command'] = st.session_state.command
save_dl_file(cmd)
return cmd, qs_cmd # returns both, latter for inline qsub, i.e. without #PBS prefix
def setup_rp():
leftcol1, centrecol1, rightcol1 = st.columns([1,1,1])
with centrecol1:
rp_info_place = st.empty()
getrp=st.checkbox("Get RP", key='getrp', help='(Re)Select RP code for programme info')
if getrp:
User_RPs = get_rp_list()
with rightcol1:
rp_info_place2 = st.empty()
if st.session_state.getrp:
if not 'rp_dict' in locals() or 'rp_dict' in globals():
rp_dict = get_rp_list()
if rp_dict:
RP_selectbox_labels = rp_dict.keys()
st.selectbox("CHPC Research Programme Code",
RP_selectbox_labels, key='user_rp',
on_change=show_rp_info(
rp_dict, rp_info_place),
help="Select to see allocation")
else:
RP_selectbox_labels = ''
st.selectbox("CHPC Research Programme Code",
RP_selectbox_labels, key='user_rp',
on_change=show_rp_info(
rp_dict, rp_info_place))
def setup_form():
form_leftcol, form_rightcol = st.columns([1,2])
with form_leftcol:
jobname = st.text_input("PBS job name",
value='JobName', key="jobname", max_chars=15,)
if st.session_state.getrp:
if st.session_state.user_rp == "":
msg = "**:red[CHPC Research Programme Code :warning:]**"
else:
msg = "CHPC Research Programme Code"
programme = st.text_input(msg, placeholder='CHPC9999',
key='programme', max_chars=8,
help='Provide your CHPC allocated RP code',
value = st.session_state.user_rp)
email = st.text_input("Email address", placeholder='[email protected]',
key='email', help="Fill in to receive job notification email")
if st.session_state.email != "": # mail events abe
lcol1, ccol1, rcol1 = st.columns(3)
with lcol1:mail_on_b = st.checkbox('b', key='mail_on_begin', help='Begin')
with ccol1:mail_on_e = st.checkbox('e', key='mail_on_end', help='End', value=True)
with rcol1:mail_on_a = st.checkbox('a', key='mail_on_abort', help='Abort')
if email:
email_opts = ''
if mail_on_a: email_opts += 'a'
if mail_on_b: email_opts += 'b'
if mail_on_e: email_opts += 'e'
st.session_state['email_opts'] = email_opts
col_left, col_right = st.columns([1,1])
with col_left:
bash = st.checkbox("Enable bash", key="bash", value=True,
help="Add bash shell to script header")
with col_right:
join = st.checkbox("Join files", key="join", value=False,
help="Combine output and error into one file")
with form_rightcol:
errorfile = st.text_input("Error file name", key='error',
help='Leave empty for generated jobname.job-id')
outfile = st.text_input("Output file name", key='out',
help="Leave empty for generated jobname.job-id" )
workdir = st.text_input("Working directory", value = 'lustre', key='workdir',
help="Fill in to change directory to this")
modules = st.text_area("Modules and initialization code",
placeholder="module load chpc/BIOMODULES python",
key='modules', help="Any other initialization")
command = st.text_input("Commandline",
placeholder="echo Hello from $(hostname) on $(date)",
key='command', help='Commands, switches and arguments')
dl_filename = st.text_input("Script file name", key='dl_filename',
label_visibility='collapsed',
value=st.session_state.jobname + '.pbs')
def submit_cli_qsub():
if not ( 'pbs' in locals() or 'pbs' in globals() ):
pbs = drmaa.Session()
try:
pbs.initialize()
except:
st.warning("Can not initialize PBS-DRMAA")
#return
else:
print("Debug: pbs not none, not initialized")
cmds = get_cli_cmds()
select = cmds['Select']
if st.session_state.place != "none":
select = select + " -l place={}".format(st.session_state.place)
if st.session_state.walltime != DEFAULT_WALLTIME:
select = select + " -l walltime=" + str(st.session_state.walltime)
jt = pbs.createJobTemplate()
jt.remoteCommand = cmds['command']
jt.jobName = st.session_state.jobname
jt.workingDirectory = st.session_state.workdir
if st.session_state.user_rp != "":
jt.nativeSpecification = select + " -P " + st.session_state.user_rp
else:
st.error("Can not run without a programme code")
return
if st.session_state.email != "":
jt.email = st.session_state.email
try:
jobid = pbs.runJob(jt)
st.success('Job has been submitted to PBS, job id **[' + jobid + ']**')
except:
st.error( 'PBS job not submitted. Check if your RP programme code is valid')
def submit_cli_qsub_ssh():
cmds = get_cli_cmds()
select = cmds['Select']
if st.session_state.place != "none":
select += " -l place={}".format(st.session_state.place)
if st.session_state.walltime != DEFAULT_WALLTIME:
select += " -l walltime=" + str(st.session_state.walltime)
if st.session_state.queue != "":
select += " -q " + st.session_state.queue
if st.session_state.user_rp != "":
select += " -P " + st.session_state.user_rp
else:
st.error("Can not run without a programme code")
return
if st.session_state.email != "":
select += " -m " + st.session_state.email
if st.session_state.command != "":
select += " -- " + st.session_state.command
try:
creds = st.session_state.user + '@' + st.session_state.server
print("DEBUG ", select )
qsub_out = run("ssh -q " + creds + \
' qsub ' + select,
capture_output=True, shell=True)
if qsub_out.returncode==0:
jobid = qsub_out.stdout.decode()
st.success('Qsub submitted to PBS, job id **[' + jobid + ']**')
else:
st.write(qsub_out.stderr.decode())
#print("DEBUG ", qsub_out.returncode )
except:
st.error( 'Qsub command not submitted')
def get_cli_cmds():
x,cmd = read_form()
return cmd
def get_qsub_cmds():
cmd, x = read_form()
return cmd
def show_preview():
cmd = get_qsub_cmds()
s=''
for k in cmd.keys():
s += cmd[k] + '\n'
st.code(s)
def show_cli_preview():
cmd = get_cli_cmds()
s='qsub '
cmd['command'] = " -- " + cmd['command']
for k in cmd.keys():
s+= ' ' + cmd[k]
st.code(s)
############################################################################################
with pbs_tab:
if not inet.up():
st.warning("No network connection")
with st.expander('PBS Job Parameters'):
setup_rp()
with st.form(key='pbs_form'):
setup_form()
#User_RPs = get_rp_list()
left1, centre1, centre2, right1 = st.columns(4)
with left1:
preview = st.form_submit_button('Preview PBS script')
with centre1:
preview_cli = st.form_submit_button('Preview qsub')
with centre2:
if inet.up():
if st.session_state.modules == "" and st.session_state.command != "":
subm_cli = st.form_submit_button('Submit qsub command')
if subm_cli:
if DRMAA_avail:
submit_cli_qsub()
else:
submit_cli_qsub_ssh()
with right1:
if DRMAA_avail:
subm_drmaa = st.form_submit_button('Submit DRMAA')
else:
subm_ssh = st.form_submit_button('Submit script',)
if preview:
show_preview()
if preview_cli:
show_cli_preview()
if 'programme' not in st.session_state.keys():
st.error("The allocated CHPC Research Programme code is required to submit jobs")
if not st.session_state.email:
st.warning("No email address given, notification mail directive omitted")
############################ End form
cmd_d=get_qsub_cmds()
text='\n'.join([cmd_d[k] for k in cmd_d.keys() ])
download = st.download_button('Download PBS script to local disk ' +\
st.session_state.dl_filename, text,
file_name=st.session_state.dl_filename)
if download:
st.info('Saving file ' + st.session_state.dl_filename)
if st.session_state.user == "user":
st.error("Please give a valid username instead of " + st.session_state.user)
else:
if 'qsub_OK' in st.session_state.keys():
if st.session_state['qsub_OK']:
if subm_ssh:
send_pbs_file(st.session_state.dl_filename)
submit_pbs_file(st.session_state.dl_filename)
print("DEBUG after submit ssh")
os.remove('/tmp/' + st.session_state.dl_filename)
else:
st.error("Qsub from PBSwif not enabled")
if 'subm_drmaa' in st.session_state.keys():
if st.session_state['subm_drmaa']:
copy_pbs_file(st.session_state.dl_filename)
submit_pbs_file(st.session_state.dl_filename)
os.remove('/tmp/' + st.session_state.dl_filename)
show_info()