def allgro(ftype, d_suff, ftop, fmdp, fin, d_rerun, o_trj, Lexe):
home = os.getenv('HOME')
p_dir = os.getcwd()
lists = os.listdir('.')
pbsfile = home + '/sandbox_gl/pypbs/sge_mdrun.tcsh'
nfile = 0
for fgro in lists:
if fgro.endswith(ftype):
nfile += 1
fname = fgro.split('.')
ndir = fname[0] + d_suff
odir = fname[0] + d_rerun
new_dir = p_dir + '/' + ndir
old_dir = p_dir + '/' + odir
os.mkdir(new_dir)
cmd = 'cp %s %s %s ' % (fgro, ftop, fmdp)
if fin:
cmd += ' %s ' % fin
cmd += ' %s ' % new_dir
print(cmd)
if Lexe or yes_or_no('%s ?' % cmd):
os.system(cmd)
if d_rerun:
f_rerun = odir + '/' + fname[0] + '.trr'
target = ndir + '/excited.trr'
cmd = 'cp %s %s' % (f_rerun, target)
if Lexe or yes_or_no('%s ?' % cmd):
os.system(cmd)
os.chdir(new_dir)
cmd = 'grompp -o %s.tpr -f %s -c %s -p %s' % (fname[0], fmdp, fgro,
ftop)
#print(cmd)
if Lexe or yes_or_no('%s ?' % cmd):
os.system(cmd)
#cmd = 'qsub -N %s -v tpr=%s %s' % (ndir,fname[0],pbsfile)
if d_rerun:
job = "rerun"
cmd = 'qsub -N %s -v tpr=%s -v job=%s -v trj=%s %s' % (
ndir, fname[0], job, ftrj, pbsfile)
else:
job = "md"
cmd = 'qsub -N %s -v tpr=%s -v job=%s %s' % (ndir, fname[0],
job, pbsfile)
if Lexe or yes_or_no('%s ?' % cmd):
os.system(cmd)
os.chdir(p_dir)
cmd = 'mv %s tmp' % fgro
os.system(cmd)
#if nfile == 1:
# return 0
return 0
def submit(qjobname, ncore, infile, amp_job, nHL, elimit, f_list, mem, ntotal,
ntr, ntype, nlist):
pwd = os.getcwd()
str_hl = " ".join(str(x) for x in nHL)
#if yes_or_no("run ?"):
#jobdir = make_dir(nHL, elimit)
if elimit == 0.0:
elimit = int(elimit)
if float(f_list[0]) == 0.0:
flimit = int(f_list[0])
else:
flimit = float(f_list[0])
### Make directory name!!
jobdir = qjobname + 'E' + str(elimit) + 'F' + str(
flimit) # +'HL'+list2str(nHL)
#jobdir = 'NC' + str(ncore) + 'HL'+list2str(nHL)+'E'+str(elimit)+'F'+str(flimit)
if jobdir in os.listdir(pwd):
print(f"{jobdir} exists")
if yes_or_no("continue ?"):
pass
else:
sys.exit(1)
else:
com = f"will you make {jobdir}?"
if yes_or_no(com):
os.mkdir(jobdir)
print(f"{jobdir} was made")
new_dir = pwd + "/" + jobdir
### cd directory
os.chdir(f"{new_dir}")
for amp_dir in amp_db:
os.system(f"ln -s {pwd}/{amp_dir} {new_dir}/{amp_dir}")
#os.system(f"cp {pwd}/OUTCAR {new_dir}")
print("amp- directories and OUTCAR were copied")
else:
com = "will you continue in here ?"
if yes_or_no(com):
pass
else:
print("exit")
sys.exit(10)
comm = amp_command(qjobname, ncore, mem, infile, amp_job, str_hl,
elimit, f_list, ntotal, ntype, nlist)
str1 = f"will you run: \n{comm}"
if yes_or_no(str1):
os.system(comm)
### Recover original directory
os.chdir(f"{pwd}")
return 0
def submit(qjobname,ncore,infile,amp_job,nHL,elimit,flimit,mem,ntotal,ntr,ntype,nlist):
pwd = os.getcwd()
str_hl = " ".join(str(x) for x in nHL)
#if yes_or_no("run ?"):
#jobdir = make_dir(nHL, elimit)
if elimit == 0.0:
elimit=int(elimit)
if flimit == 0.0:
flimit=int(flimit)
### Make directory name!!
#jobdir = 'HL'+list2str(nHL)+'E'+str(elimit)+'F'+str(flimit)
jobdir = 'NC' + str(ncore) + 'HL'+list2str(nHL)+'E'+str(elimit)+'F'+str(flimit)
if jobdir in os.listdir(pwd):
print(f"{jobdir} exists")
if yes_or_no("continue ?"):
pass
else:
sys.exit(1)
else:
com = f"will you make {jobdir}?"
if yes_or_no(com):
os.mkdir(jobdir)
print(f"{jobdir} was made")
new_dir = pwd + "/" + jobdir
### cd directory
os.chdir(f"{new_dir}")
for amp_dir in amp_db:
os.system(f"ln -s {pwd}/{amp_dir} {new_dir}/{amp_dir}")
#os.system(f"cp {pwd}/OUTCAR {new_dir}")
print("amp- directories and OUTCAR were copied")
else:
print("exit")
sys.exit(10)
comm = f"qsub -N {qjobname}"
comm += f" -pe numa {ncore} -l mem={mem} -v fname={infile} -v pyjob={amp_job} -v hl=\"{str_hl}\" -v el={elimit} -v fl={flimit} -v nc={ncore}"
comm += " -v ndata=" + ' '.join(ntotal)
comm += f" -v dtype={ntype} "
comm += " -v dlist='" + ' '.join(nlist) + "'"
comm += " $SB/pypbs/sge_amp.csh"
str1 = f"will you run: \n{comm}"
if yes_or_no(str1):
os.system(comm)
### Recover original directory
os.chdir(f"{pwd}")
return 0
def run_job(job, ifile, eoption, nskip, pbctype):
pdir = os.getcwd()
if not os.path.isfile(ifile):
print("there is no %s" % ifile)
exit(10)
f_pre, f_ext = common.fname_decom(ifile)
L_write = False
q = "overwrite ? "
if job == 'ene':
if os.path.isfile('%s.xvg' % f_pre):
print("%s.xvg exists: " % f_pre)
if common.yes_or_no(q):
L_write = True
else:
L_write = True
if L_write:
com = "g_energy -f %s.edr -dp -o %s.xvg " % (f_pre, f_pre)
print(com)
os.system(com)
if os.path.isfile('%s.xvg' % f_pre):
print("%s.xvg was made" % f_pre)
else:
print("job failed")
return 0
elif job == 'trj':
if os.path.isfile('%s.gro' % f_pre):
print("%s.gro exists: " % f_pre)
if common.yes_or_no(q):
L_write = True
else:
L_write = True
if L_write:
com = "trjconv -f %s.trr -s %s.tpr -o %s.gro -skip %d -pbc %s" % (
f_pre, f_pre, f_pre, nskip, pbctype)
print(com)
q2 = "will you run?"
if common.yes_or_no(q2):
os.system(com)
print("%s.gro was made" % f_pre)
else:
print("job aborted")
return 0
def find_inputfile(pwd, job):
if os.path.isfile('OUTCAR'):
fname = 'OUTCAR'
else:
for f in os.listdir(pwd):
if f.endswith('extxyz'):
fname = f
break
quest = f"file {fname} will be read with job='{job}' ?"
if yes_or_no(quest):
return fname
else:
return 0
def jobs(job, job_level, model, nfile, Llink, link_file, f3_option, Lnbo,
nao_chg, nao_chgsum, Lrun):
One_model = class_dic[model]
model_name = "m" + str(model)
if job == "moc":
if nfile == 1:
files = One_model.nf1
elif nfile == 3:
if not f3_option:
files = One_model.nf3
else:
files = One_model.nf3_
elif nfile == 5:
files = One_model.nf5
at_type, mo_type = One_model.atom_type(nfile)
link = ""
if Llink:
link += " -l "
elif link_file:
link += f" -lf {model_name}-{nfile}f.dat"
com = f"mplot_mo.py -f {files} -a {at_type} -t {mo_type} {link}"
if yes_or_no(com + " ::will you run?"):
os.system(com)
elif job == "nbo":
mfiles = " ".join([m1.f3, m2.f3, m3.f3, m4.f3, m5.f3, m6.f3])
atoms = " ".join(nao_chg)
chgsum = " ".join(nao_chgsum)
com = f"mplot_mo.py -f {mfiles} --{job} -ncg {atoms} -ncs {chgsum}"
if job_level > 1:
com += " | grep SUM | awk '{print $4}'"
print("-js 2 for sum, 3 for plot")
if yes_or_no(com +
" ::will you run? (for more option: use -js [int>1]"):
os.system(com)
return 0
def alldir(ftype, d_suff, d_pre, Lexe):
p_dir = os.getcwd()
lists = os.listdir('.')
nfile = 0
for sdir in lists:
if sdir.startswith(d_pre):
nfile += 1
print(sdir)
d_id = sdir.split('_')
id_sys = d_id[0]
#odir = fname[0]+d_rerun
dname = p_dir + '/' + sdir
os.chdir(dname)
cmd = "echo 9 | g_energy -f %s.edr -o %s" % (id_sys, "pot")
if Lexe or yes_or_no("%s ?" % cmd):
os.system(cmd)
"""
os.mkdir(new_dir)
cmd = 'cp %s %s %s ' % (fgro, ftop, fmdp)
if fin:
cmd += ' %s ' % fin
cmd += ' %s ' % new_dir
print(cmd)
if Lexe or yes_or_no('%s ?' % cmd):
os.system(cmd)
os.chdir(new_dir)
cmd = 'grompp -o %s.tpr -f %s -c %s -p %s' % (fname[0],fmdp,fgro,ftop)
#print(cmd)
if Lexe or yes_or_no('%s ?' % cmd):
os.system(cmd)
#cmd = 'qsub -N %s -v tpr=%s %s' % (ndir,fname[0],pbsfile)
if d_rerun:
job = "rerun"
cmd = 'qsub -N %s -v tpr=%s -v job=%s -v trj=%s %s' % (ndir,fname[0],job,ftrj,pbsfile)
else:
job = "md"
cmd = 'qsub -N %s -v tpr=%s -v job=%s %s' % (ndir,fname[0],job,pbsfile)
if Lexe or yes_or_no('%s ?' % cmd):
os.system(cmd)
cmd = 'mv %s tmp' % fgro
os.system(cmd)
"""
os.chdir(p_dir)
#if nfile == 1:
# return 0
return 0
def main():
parser = argparse.ArgumentParser(description='run amp with extxyz, OUTCAR: validation is removed ', prefix_chars='-+/')
parser.add_argument('-f', '--infile', help='ASE readible file: extxyz, OUTCAR(VASP) ')
parser.add_argument('-j', '--job', default='tr', choices=['tr','te','pr','pt'], help='job option:"train","test","md","profile","plot"')
#parser.add_argument('-a', '--all_fig', action="store_true", help='if job==te, include all figures')
parser.add_argument('-p', '--pot', default="amp.amp", help="input amp potential")
### data selection
data_group = parser.add_argument_group()
#data_group.add_argument('-d','--data_mine', action="store_true", help='if true, use data interval')
data_group.add_argument('-di','--data_list', type=int, nargs='+', help='data interval list')
data_group.add_argument('-dm','--data_mine', type=int, nargs='+', help='data interval list')
data_group.add_argument('-ds','--dnsets',default=5,type=int, help='num of sets:1 train all sets, otherwise, last set is for test')
### others
parser.add_argument('-nm','--nmol',default=1,type=int,help='num of molecules in the system to normalize error')
parser.add_argument('-hl', '--hidden_layer', nargs='*', type=int, default=[8,8,8], help='Hidden Layer of lists of integer')
parser.add_argument('-el', '--e_conv', default=0.001, type=float, help='energy convergence limit')
parser.add_argument('-fl', '--f_conv', default=0.01, type=float, help='force convergence limit')
parser.add_argument('-tx', '--twinx', action="store_false", help='turn off to use twinx of two y-axes')
parser.add_argument('-g', action="store_false", help='if val default is False, otherwise True')
parser.add_argument('+g', action="store_true", help='if val default is False, otherwise True')
parser.add_argument('-nc', '--ncore', default=1, type=int, help='number of core needs to be defined')
args = parser.parse_args()
if args.data_list:
data_int = args.data_list
else:
data_int = args.dnsets
pwd = os.getcwd()
if args.infile:
fname=args.infile
else:
if os.path.isfile('OUTCAR'):
fname = 'OUTCAR'
else:
for f in os.listdir(pwd):
if f.endswith('extxyz'):
fname = f
break
quest = f"file {fname} will be read with job='{args.job}' ?"
if yes_or_no(quest):
pass
else:
sys.exit(1)
amp_jobs(fname,args.job,data_int,args.pot,args.hidden_layer,args.e_conv,args.f_conv,args.g,args.ncore,args.nmol,args.twinx)
return
def run(dir1, dir2, files, L_run):
load_files = []
home = os.getenv('HOME')
if not dir1:
dir1 = "/shared/share_win/web_load/"
if not dir2:
dir2 = home + "/public_html/research/"
if not files:
load_files = os.listdir(dir1)
else:
load_files = files
for f in load_files:
fname = dir1 + f
com = "cp %s %s" % (fname, dir2)
if L_run or yes_or_no(com):
os.system(com)
return 0
def grom_pp(fpre, mfile, mdyn, fgro):
print("Do Grmx preprocess in a given system")
ftarget = fpre + "_" + mdyn
cmd = "grompp -f %s -c %s -p %s.top -o %s.tpr" % (mfile, fgro, fpre,
ftarget)
print(cmd)
print("-f input .mdp")
print("-c input .gro, grmx coordinate")
print("-p input .top")
print("-o output .tpr for MDrun")
q2 = "will you run ? "
if common.yes_or_no(q2):
os.system(cmd) # this does not make .tpr
if os.path.isfile('%s.tpr' % ftarget):
print("%s.tpr was made" % ftarget)
return 1
else:
print("Fail to generate %s.tpr" % ftarget)
else:
print("Job terminated")
return 0
def amp_work(work, qjobname, ncore, infile, amp_job, nHL, max_hl, elimit,
f_list, mem, ntotal, ntr, ntype, nlist):
### Make subdir and run
if work == 'scan':
hl_lists = HL_list(max_hl, *nHL)
for hlist in hl_lists:
qname = get_qname_suff(qjobname, *hlist)
submit(qname, ncore, infile, amp_job, hlist, elimit, f_list, mem,
ntotal, ntr, ntype, nlist)
elif work == 'onejob':
qname = get_qname(qjobname, *nHL)
submit(qname, ncore, infile, amp_job, nHL, elimit, f_list, mem, ntotal,
ntr, ntype, nlist)
### make database without making subdirectory
else:
str_hl = " ".join(str(x) for x in nHL)
comm = amp_command(qjobname, ncore, mem, infile, amp_job, str_hl,
elimit, f_list, ntotal, ntype, nlist)
str1 = f"will you run: \n{comm}"
if yes_or_no(str1):
os.system(comm)
return 0
def run_job(job, ifile, icharge, mdfile, dyn, jobname, grofile):
pdir = os.getcwd()
if not os.path.isfile(ifile):
print("there is no %s" % ifile)
exit(10)
f_pre, f_ext = common.fname_decom(ifile)
L_write = False
q = "continue to overwrite ? "
q2 = "will you run ? "
### step 1: make .pdb file
if job == 'mol2pdb':
if os.path.isfile('%s.pdb' % f_pre):
print("%s.pdb exists: " % f_pre)
if common.yes_or_no(q):
L_write = True
else:
L_write = True
if L_write:
com = "mol2pdb.pl %s.in > %s.pdb " % (f_pre, f_pre)
print(com)
q1 = "will you make .pdb from .in(q-chem) ?"
print("input: \"a.in\"\noutput: \"a.pdb\"")
if common.yes_or_no(q1):
os.system(com)
print("Step 1: %s.pdb was made" % f_pre)
print("continue to Step 2: pdb2mol2")
else:
print("job was terminated")
return 0
### step 2: make .mol2 file
elif job == 'pdb2mol2':
if os.path.isfile('%s.mol2' % f_pre):
print("%s.mol2 exists: " % f_pre)
if common.yes_or_no(q):
L_write = True
else:
L_write = True
if L_write:
print("input: \"a.pdb\"\noutput: \"a.mol2\"")
print("net charge: %d" % icharge)
print("atom type: gaff")
print("to modify more, correct source code")
com = "antechamber -i %s.pdb -fi pdb -o %s.mol2 -fo mol2 -at gaff -c bcc -nc %d" % (
f_pre, f_pre, icharge)
print("%s \n This job will take time" % com)
q1 = "will you make .mol2 from .pdb ?"
if common.yes_or_no(q1):
os.system(com)
print("%s.mol2 was made" % f_pre)
print("continue to make frcmod step 3: frcmod")
else:
print("job was terminated")
return 0
### Step 3: make .frcmod file
elif job == 'frcmod':
if os.path.isfile('%s.frcmod' % f_pre):
print("%s.frcmod exists: " % f_pre)
if common.yes_or_no(q):
L_write = True
else:
L_write = True
if L_write:
com = "parmchk2 -i %s.mol2 -f mol2 -s 1 -o %s.frcmod" % (f_pre,
f_pre)
print(com)
print("-i for input file")
print("-f for input format")
print("-s for FF parameter set")
print("-o for frcmod output file")
q1 = "will you make .frcmod from .mol2 ?"
if common.yes_or_no(q1):
os.system(com)
print("%s.frcmod was made" % f_pre)
print("continue to check mol2 charge w mol2_chg")
else:
print("job was terminated")
return 0
### Step 4: check .mol2-charge then go to tleap
elif job == "mol2chg":
com = 'cal_chg.sh %s' % ifile
print("check total charge of %s" % ifile)
os.system(com)
q1 = "is charge OK ?"
if common.yes_or_no(q1):
print("Alert:: tleap is interactive mode, Do this on shell")
print("$tleap")
print("tleap> source leaprc.gaff")
print("tleap> mod = loadamberparams %s.frcmod" % f_pre)
print("tleap> x = loadmol2 %s.mol2" % f_pre)
print("tleap> saveamberparm x %s.top %s.crd" % (f_pre, f_pre))
print("tleap> quit")
print("with %s.top %s.crd, go to step 5: amber2grmx" %
(f_pre, f_pre))
else:
print("job was terminated")
print("modify %s.mol2 then go to Step 4: mol2_chg again")
return 0
### step 5: tleap-made .top and .crd. make gmx.top, gmx.gro
elif job == "amber2grmx":
q1 = "top, crd were made from tleap ? "
if common.yes_or_no(q1):
if os.path.isfile("%s.top" % f_pre) and os.path.isfile(
"%s.crd" % f_pre):
com = "acpype.py -p %s.top -x %s.crd" % (f_pre, f_pre)
print(com)
print("-i for input but not used here")
print("-p amber parameter topology, always used with -x")
print("-x amber input coordinate, always used with -p")
os.system(com)
print("_GMX.top, _GMX.gro were made")
else:
print("this work is not ready")
exit(44)
q1 = "will you arrange directory ? "
if common.yes_or_no(q1):
tmpdir = pdir + "/qc_input"
if not os.path.isdir(tmpdir):
os.mkdir(tmpdir)
os.system("mv %s/* %s" % (pdir, tmpdir))
os.chdir(tmpdir)
os.system("cp *GMX* %s" % pdir)
os.chdir(pdir)
print("change gro and top file to a proper names")
print(
"modify .gro for box size: use ins/substitute mode to keep format"
)
print("editconf to move the system to center if necessary")
print("modify .top charge again: got to Step 5.1 \"topchg\"")
return 0
### Step 5.1: check gromax.top charge then continue
elif job == "topchg":
print("check gromac %s.top charge" % f_pre)
com = "cal_chg.sh %s" % ifile
os.system(com)
print(
"check or modify %s.top file then go to Step 6 to make water box: waterbox"
% f_pre)
return 0
### step 6: make water box in gromacs .top .gro
elif job == "waterbox":
print("it will fill water in the box")
com = "genbox -cp %s.gro -cs spc216.gro -o %s_sol.gro -p %s.top" % (
f_pre, f_pre, f_pre)
print(com)
print("-cp input for gro structure file with proper box size")
print("-cs input for sovent water structure")
print("-o output for _sol.gro")
print("-p in/out topology file is overwritten")
q1 = "will you run ? "
if common.yes_or_no(q1):
os.system(com)
print("%s_sol.gro was made" % f_pre)
print("%s.top was overwritten" % f_pre)
print("modify .top for water, Step 7 : top_gaff_addwater")
else:
print("The job was terminated")
return 0
### Step 7: modify .top for water before making pp
elif job == "modtop_water":
print("modify .top file on the fly")
if f_ext != "top":
print("input .top")
exit(55)
cmd = "top_gaff_add_water.sh %s.top" % f_pre
os.system(cmd)
print("Continue to step 8 with %s_sol.gro: pre_pp" % f_pre)
return 0
### step 8: make MD inputfile of .tpr for system without anion
elif job == "pre_pp":
if f_ext != "top":
print("input .top")
exit(56)
if not mdfile:
print("input mdfile using --md")
exit(57)
print("Do Grmx preprocess in a given system")
if grofile:
gfile = grofile
else:
gfile = f_pre + "_sol.gro"
Lsuccess = grom_pp(f_pre, mdfile, dyn, gfile)
if Lsuccess:
print(
"Continue to modify .top before adding anion to system, step 9: top_gaff_addion"
)
return 0
### stop 9: add anion to MD input file
elif job == "modtop_ion":
if f_ext != "top":
print("input .top")
exit(55)
print("modify .top file on the fly for adding ion")
cmd = "top_gaff_add_ion.sh %s.top" % f_pre
print(cmd)
os.system(cmd)
print("%s.top was modified" % f_pre)
print("-- Add ion interactively: -- ")
cmd = "genion -s %s.tpr -o %s_sol_neut.gro -p %s.top -nn 1 -nname CL -nq -1" % (
f_pre, f_pre, f_pre)
print(cmd)
print("-s input of MD running file")
print("-o output .gro of coordination")
print("-p in/out .top overwritten")
q1 = "will you run interactive commander genion ?"
if common.yes_or_no(q1):
os.system(cmd)
print(
"after made %s_sol_neut.gro, make .tpr again: go to step 10 using make_pp"
% f_pre)
return 0
### step 10: make pp
if job == 'do_pp':
if f_ext != "top":
print("input .top")
exit(96)
if not mdfile:
print("input mdfile using --md")
exit(97)
if grofile:
gfile = grofile
else:
gfile = f_pre + "_sol_neut.gro"
Lsuccess = grom_pp(f_pre, mdfile, dyn, gfile)
if Lsuccess:
print("Complete %s_%s.tpr was made: ready to run MD" %
(f_pre, dyn))
print(
"submit a job with -v variable, 'submit': qsub -N jobname -v tpr=jobname sge_mdrun.tcsh"
)
print("note: use .tcsh: bash script .sh cannot be used")
print("Or submit at last step:: 'submit'")
return 0
### Step last: submit a job
if job == 'submit':
home = os.environ['HOME']
pbs = home + '/sandbox_gl/pypbs/sge_mdrun.tcsh'
#print(home)
### jobname makes directory
tgro = pdir + '/' + f_pre + ".gro"
if f_ext != "tpr":
print("run with .tpr name")
exit(99)
elif os.path.isfile(tgro):
print("do not overwrite %s.gro" % f_pre)
exit(98)
if jobname:
jname = jobname
job_dir = pdir + '/' + jname
os.mkdir(job_dir)
fname = pdir + '/' + f_pre + '.tpr'
copy(fname, job_dir)
os.chdir(job_dir)
else:
#jname = f_pre
print("try job name with -n or --jobname")
exit(100)
cmd = "qsub -N %s -v tpr=%s %s" % (jname, f_pre, pbs)
print(cmd)
print("job: mdrun -s %s.tpr -c %s.gro -o %s.trr -e %s.edr -g %s.log" %
(f_pre, f_pre, f_pre, f_pre, f_pre))
print("input: %s.tpr" % f_pre)
print("output: %s.gro, %s.trr, %s.edr, %s.log" %
(f_pre, f_pre, f_pre, f_pre))
q = 'submit this job ?'
if common.yes_or_no(q):
os.system(cmd)
print("job submited.")
else:
print("job skipped")
return 0
def jobs(work, fname, Lrun, quejob, np, nmem, que):
if work == None:
mdir = os.path.dirname(__file__)
print(f"List directory in {mdir}")
exe, mod = dir_files(mdir)
print("Executable:: ")
exe_s = sorted(exe)
mod_s = sorted(mod)
for f in exe_s:
print(" {}".format(f))
print("Module:: ")
for f in mod_s:
print(" {}".format(f))
print(
"#Comment for sge: -w [sge|amp|grmx|qchem|sleep|qsub for arguments]"
)
print(" AMP:: sge_amp.tcsh")
print(" Gromacs:: sge_mdrun2.tcsh")
print(" Q-Chem:: sge_qchem.csh")
print(" dummy job:: sge_sleep.csh")
elif work == 'sge':
print(" $qstat -f # see all nodes(/used/total) and my job")
print(" $qstatf # aliast qstat -f ...")
print(" $qfree # free nodes")
print(
" $qhist # shows number of running cores and jobs in Queue"
)
print(" $qmem # memory")
elif work == 'qsub':
print(
" qsub -N jobname -v var=a_variable /gpfs/home/joonho/sandbox_gl/pypbs/sge_qchem.csh"
)
print("\t$var can be used as variable in the script")
print("\tscript name will be full name")
elif work == 'qchem':
### version control
#com = f" qsub -N {quejob} -v qcjob={fname} -v ver=\"5.1p\" -v nc={np} -pe numa {np} /gpfs/home/joonho/sandbox_gl/pypbs/sge_qchem.csh"
if fname == None:
com = f" qsub -N {quejob} -v qcjob=a.in -v nc={np} -pe numa {np} /gpfs/home/joonho/sandbox_gl/pypbs/sge_qchem.csh"
else:
com = f" qsub -N {quejob} -v qcjob={fname} -v nc={np} -pe numa {np} /gpfs/home/joonho/sandbox_gl/pypbs/sge_qchem.csh"
print(com)
if not Lrun:
print("\tuse -r to queue submit")
print(" \"{}\" is aliased to \"{}\"".format(
os.path.basename(__file__) + " -w qchem", "qchem_run"))
print(
" use :: qchem_run -j Queue-jobname -f qin-file -n num_process"
)
print(" e.g.:: qchem_run -jopt -fCO2 -n4")
print(" version:: use 3.1 for jmol and 5.1 for all the keywords")
print(
" For batch::\n\tdir_run.sh in \# $1 for qchem input type")
if fname == None:
print(
f" in script::\n\t/gpfs/home/joonho/sciware/qchem5.1p/bin/qchem -np {np} a.in a.out"
)
else:
print(
f" in script::\n\t/gpfs/home/joonho/sciware/qchem5.1p/bin/qchem -np {np} {fname}.in {fname}.out"
)
print("\tenv variable such as $QC is not working in script")
else:
q = "will you run?"
if yes_or_no(q):
os.system(com)
elif work == 'grmx':
print(" qsub -v tpr=mdname sge_mdrun2.sh")
elif work == 'amp':
print("SGE validation::")
print(
f" qsub -v fname={fname} -v py_job=val -v scan=scan -v nc={np} -q {que} -pe numa {np} -l h_vmem={nmem} $SGE_HOME/sge_amp.csh"
)
print("\tpy_job for [validation||train||test]")
print(
"\tscan variable (if exists) average for several trial with the same [HL, ene convergency]"
)
print("\tsetenv SGE_HOME $HOME/sandbox_gl/pypbs")
print("\tfind node:: sge_nodes.py || qstat -f")
print(
" in script::\n\tsetenv PYTHONPATH $HOME/sandbox_gl/pycommon:$HOME/sandbox_gl/mymplot"
)
print("\tset PYTHON = \"$HOME/anaconda3/bin/python\"")
print("\tset EXE = \"$HOME/sandbox_gl/py_ai/amp_ene.py\"")
print("\t$PYTHON $EXE $fname $py_job -hl 4 4 4 -el 0.001 -n 5 -g")
elif work == 'qsleep':
print("Dummy job::")
print(
f" qsub -q {que} -pe numa {np} -l mem={nmem} $SB/pypbs/sge_sleep.csh"
)
print(
" Sample: qsub -q qname(sandy@slet02) -pe numa 6(num of process) -l mem=24G $SB/pypbs/sge_sleep.csh"
)
return