def execute(self):
Flag=True
modcmd="tests/bash_module_test.bash"
output=capture(modcmd)
if "not found" in output:
self.error_message+=" Error: Module is not defined."
return False
modcmd="tests/csh_module_test.csh"
output=capture(modcmd)
if not output:
self.error_message+=" Error: Module is not defined."
return False
unknown = "**UNKNOWN**"
value = os.environ.get('LMOD_CMD',unknown)
if (value == unknown):
self.error_message+=" Error: Module is not defined."
return False
lmodcmd=os.environ['LMOD_CMD']
mlcmd=lmodcmd + " python list"
output=captureErr(mlcmd).split()
module_need=["TACC","TACC-paths","Linux","cluster"]
for mod1 in module_need:
if mod1 not in output:
self.error_message+=" Error: Module \"%s\" is not loaded.\n" %mod1
Flag=False
return Flag
def execute(self):
Flag=True
modcmd="tests/bash_module_test.bash"
output=capture(modcmd)
if "not found" in output:
self.error_message+="\tError: Module is not defined."
return False
modcmd="tests/csh_module_test.csh"
output=capture(modcmd)
if not output:
self.error_message+="\tError: Module is not defined."
return False
unknown = "**UNKNOWN**"
value = os.environ.get('LMOD_CMD',unknown)
if (value == unknown):
self.error_message+="\tError: Module is not defined."
return False
lmodcmd=os.environ['LMOD_CMD']
mlcmd=lmodcmd + " python list"
output=captureErr(mlcmd).split()
module_need=["TACC"]
# print(output)
for mod1 in module_need:
if not any(mod1 in tmpstr for tmpstr in output):
self.error_message+="\tError: Necessary module \"%s\" is not loaded.\n" %mod1
Flag=False
return Flag
def __init__(self, exec_progA):
ignoreT = {
'env' : True,
'time' : True,
}
cmd = None
for prog in exec_progA:
bare = os.path.basename(prog)
if (not (bare in ignoreT)):
cmd = prog
break
self.__execName = which(cmd)
ldd = None
if (self.__execName):
outStr = capture(["file", self.__execName])
if (outStr.find("ASCII text") > 0):
self.__execType = "script"
elif (outStr.find("executable") > 0):
self.__execType = "binary"
ldd = capture(["ldd", self.__execName])
else:
self.__execType = None
info = os.stat(self.__execName)
self.__modify = info.st_mtime
self.__libA = self.__parseLDD(ldd)
self.__hash = self.__computeHash(self.__execName)
def __init__(self, exec_progA):
ignoreT = {
'env' : True,
'time' : True,
}
cmd = None
for prog in exec_progA:
bare = os.path.basename(prog)
if (not (bare in ignoreT)):
cmd = prog
break
self.__execType = None
self.__execName = which(cmd)
self.__libA = []
if (self.__execName):
outStr = capture(["file", self.__execName])
if (outStr.find("script") > 0 or outStr.find("text") > 0):
self.__execType = "script"
else:
self.__execType = "binary"
ldd = capture(["ldd", self.__execName])
self.__libA = self.__parseLDD(ldd)
info = os.stat(self.__execName)
self.__modify = info.st_mtime
self.__hash = self.__computeHash(self.__execName)
def execute(self):
result = True
# home = os.environ['HOME']
userid=capture("whoami").rstrip()
# grepcmd="grep %s /etc/passwd | cut -d ':' -f6" %userid
grepcmd="/bin/awk -F: -v user=%s '$1 == user {print $6}' </etc/passwd" %userid
home=capture(grepcmd)
if not home:
self.error_message+="\tError: Your home directory is inaccessible!\n"
return False
home=home[:-1]
sshD = os.path.join(home,".ssh")
dirA = [ home, sshD ]
if not os.path.isdir(sshD):
self.error_message+="\tError: .ssh directory does not exist or is inaccessible!\n"
return False
keyfile=os.path.join(sshD,"authorized_keys")
if not os.path.isfile(keyfile):
self.error_message+="\tError: Authorized key file does not exist or is inaccessible!\n"
return False
# The following part is a little wordy, because we want to make some customized error messages:
a = self.__write_group_other_test(home)
for entry in a:
if (entry['value']):
result = False
self.error_message+="\tError: "+entry['name']+ " permission on $HOME will cause RSA to fail!\n"
#remove entry['name'] in the Error message on July 22, 2015
a = self.__read_user_test(home)
for entry in a:
if (entry['value']):
result = False
self.error_message+="\tError: no user read permission on $HOME will cause RSA to fail!\n"
# The following part is a little wordy, because we want to make some customized error messages:
a = self.__write_group_other_test(sshD)
for entry in a:
if (entry['value']):
result = False
self.error_message+="\tError: "+entry['name']+ " permission on $HOME/.ssh will cause RSA to fail!\n"
#remove entry['name'] in the Error message on July 22, 2015
a = self.__read_user_test(sshD)
for entry in a:
if (entry['value']):
result = False
self.error_message+="\tError: no user read permission on $HOME/.ssh will cause RSA to fail!\n"
# test owner and perm on ~/.ssh/authorized_keys
r = self.__authorized_keys_test(keyfile)
if (r):
result = False
self.error_message+="\tError: The permission and/or ownership on " + keyfile +" will cause RSA to fail!\n"
return result
def execute(self):
userid=capture("whoami").rstrip()
host=syshost()
if (host=="stampede" or host=="ls5"):
spaces=["/home1","/work"]
elif host=="ls4":
spaces=["/home1","/work"]
elif (host=="maverick"):
spaces=["/home","/work"]
else:
return True
Flag=True
for space in spaces:
if ( (host=="ls4" and space=="/home1") or (host=="maverick" and space=="/home") or (host=="ls5" and space=="/home1")):
quotacmd="quota"
rawinfo=capture(quotacmd).split("\n")
if len(rawinfo)<3:
return False
quotainfo=rawinfo[-2].split()
## print(quotainfo[0],quotainfo[2],quotainfo[3],quotainfo[5])
## print(quotainfo)
## if len(quotainfo) <6:
if len(quotainfo) <6 or (not (quotainfo[0]).isdigit()):
self.error_message+="\tError: "+"No valid quota report\n"
return False
if float(quotainfo[0]) >= float(quotainfo[2])*0.95 :
Flag=False
self.error_message+="\tError: You are over/close to the disk limit under %s.\n" %space
if float(quotainfo[3]) >= float(quotainfo[5])*0.95 :
Flag=False
self.error_message+="\tError: You are over/close to the inode limit under %s.\n" %space
else:
lfscmd="lfs quota -u %s %s" %(userid,space)
## print(lfscmd)
quotainfo=capture(lfscmd).split("\n")[2].split()
quotainfo[5]=quotainfo[5].strip("*")
quotainfo[1]=quotainfo[1].strip("*")
## print(quotainfo[1], quotainfo[3], quotainfo[5], quotainfo[7]
## print(quotainfo)
if len(quotainfo) <8:
self.error_message+="\tError: "+"No valid quota report\n"
return False
if float(quotainfo[1]) >= float(quotainfo[3])*0.95 :
Flag=False
self.error_message+="\tError: You are over/close to the disk limit under %s.\n" %space
if float(quotainfo[5]) >= float(quotainfo[7])*0.95 :
Flag=False
self.error_message+="\tError: Your are over/close to the inode limit under %s.\n" %space
return Flag
def execute(self):
userid=capture("whoami").rstrip()
host=syshost()
if (host=="stampede2" or host=="ls5"):
spaces=["/home1","/work"]
elif host=="ls4":
spaces=["/home1","/work"]
elif (host=="maverick"):
spaces=["/home","/work"]
else:
return True
Flag=True
for space in spaces:
if ( (host=="ls4" and space=="/home1") or (host=="maverick" and space=="/home") or (host=="ls5" and space=="/home1")):
quotacmd="quota"
rawinfo=capture(quotacmd).split("\n")
if len(rawinfo)<3:
return False
quotainfo=rawinfo[-2].split()
## print(quotainfo[0],quotainfo[2],quotainfo[3],quotainfo[5])
## print(quotainfo)
if len(quotainfo) <6 or (not (quotainfo[0]).isdigit()):
self.error_message+="\tError: "+"No valid quota report\n"
return False
if float(quotainfo[0]) >= float(quotainfo[2])*0.9 :
Flag=False
self.error_message+="\tError: You are over/close to the disk limit under %s.\n" %space
if float(quotainfo[3]) >= float(quotainfo[5])*0.9 :
Flag=False
self.error_message+="\tError: You are over/close to the inode limit under %s.\n" %space
else:
lfscmd="lfs quota -u %s %s" %(userid,space)
## print(lfscmd)
quotainfo=capture(lfscmd).split("\n")[2].split()
quotainfo[5]=quotainfo[5].strip("*")
quotainfo[1]=quotainfo[1].strip("*")
## print(quotainfo[1], quotainfo[3], quotainfo[5], quotainfo[7]
## print(quotainfo)
if len(quotainfo) <8:
self.error_message+="\tError: "+"No valid quota report\n"
return False
if float(quotainfo[1]) >= float(quotainfo[3])*0.85 :
Flag=False
self.error_message+="\tError: You are over/close to the disk limit under %s.\n" %space
if float(quotainfo[5]) >= float(quotainfo[7])*0.85 :
Flag=False
self.error_message+="\tError: Your are over/close to the inode limit under %s.\n" %space
return Flag
def __parseLDD(self, ldd):
if (ldd.find("not a dynamic executable") > 0):
return []
lineA = ldd.split('\n')
libA = []
d = {}
for line in lineA:
fieldA = line.split()
N = len(fieldA)
if (N < 1):
break
elif (N == 4):
lib = fieldA[2]
else:
lib = fieldA[0]
lib = os.path.realpath(lib)
d[lib] = True
libA = d.keys()
libA = sorted(libA)
libB = []
for lib in libA:
hash_line = capture(['sha1sum', lib])
if (hash_line.find("No such file or directory") != -1):
v = "unknown"
else:
v = hash_line.split()[0]
libB.append([lib, v])
return libB
def main():
try:
uuid = sys.argv[ 1]
status = sys.argv[ 2]
wd = sys.argv[ 3]
syshost = sys.argv[ 4]
pstree = sys.argv[ 5]
execname = sys.argv[ 6]
xaltobj = sys.argv[ 7]
build_epoch = sys.argv[ 8]
linklineFn = sys.argv[ 9]
resultFn = sys.argv[10]
if (execname.find("conftest") != -1):
return 1
hash_line = capture(['sha1sum', execname])
if (hash_line.find("No such file or directory") != -1):
return 1
hash_id = hash_line.split()[0]
# Step one clean up linkline data
sA = cleanup(xaltobj, linklineFn)
resultT = {}
resultT['uuid'] = uuid
resultT['link_program'] = extract_compiler(pstree)
resultT['build_user'] = os.environ['USER']
resultT['exit_code'] = status
resultT['build_epoch'] = build_epoch
resultT['exec_path'] = os.path.abspath(execname)
resultT['hash_id'] = hash_id
resultT['wd'] = wd
resultT['build_syshost'] = syshost
resultT['linkA'] = sA
dirname,fn = os.path.split(resultFn)
tmpFn = os.path.join(dirname, "." + fn)
if (not os.path.isdir(dirname)):
os.mkdir(dirname);
s = json.dumps(resultT, sort_keys=True, indent=2, separators=(',',': '))
f = open(tmpFn,'w')
f.write(s)
f.write("\n")
if (hash_line.find("sha1sum:") != -1):
f.write(hash_line)
f.close()
os.rename(tmpFn, resultFn)
except:
logger.exception("XALT_EXCEPTION:xalt_generate_linkdata")
return 0
def execute(self):
result = True
pub_key = capture('cat ~/.ssh/id_rsa.pub').replace('\n','')
cmd = "grep -F \"%s\" ~/.ssh/authorized_keys > /dev/null 2>&1" % pub_key
status = run_cmd(cmd)
if (status != 0):
self.error_message+=" Error: ~/.ssh/id_rsa.pub not found in ~/.ssh/authorized_keys.\n"
return False
cmd2 ="awk '{if ($1!=\"ssh-dss\" && $1!=\"ssh-rsa\" || NF <= 1) print $0}' ~/.ssh/authorized_keys"
cmd2_out = capture(cmd2)
if cmd2_out:
self.error_message+=" Error: ~/.ssh/authorized_keys includes invalid or broken key(s).\n"
return False;
return result
def execute(self):
result = True
pub_key = capture('cat ~/.ssh/id_rsa.pub').replace('\n', '')
cmd = "grep -F \"%s\" ~/.ssh/authorized_keys > /dev/null 2>&1" % pub_key
status = run_cmd(cmd)
if (status != 0):
self.error_message += "\tError: ~/.ssh/id_rsa.pub not found in ~/.ssh/authorized_keys.\n"
return False
cmd2 = "awk '{if ($1!=\"ssh-dss\" && $1!=\"ssh-rsa\" || NF <= 1) print $0}' ~/.ssh/authorized_keys"
cmd2_out = capture(cmd2)
if cmd2_out:
self.error_message += "\tError: ~/.ssh/authorized_keys includes invalid or broken key(s).\n"
return False
return result
def execute(self):
result = True
# home = os.environ['HOME']
userid=capture("whoami").rstrip()
# grepcmd="grep %s /etc/passwd | cut -d ':' -f6" %userid
grepcmd="/bin/awk -F: -v user=%s '$1 == user {print $6}' </etc/passwd" %userid
home=capture(grepcmd)
if not home:
self.error_message+=" Error: Can not find home directory!\n"
return False
home=home[:-1]
sshD = os.path.join(home,".ssh")
dirA = [ home, sshD ]
if not os.path.isdir(sshD):
self.error_message+=" Error: .ssh directory does not exist or is inaccessible!\n"
return False
keyfile=os.path.join(sshD,"authorized_keys")
if not os.path.isfile(keyfile):
self.error_message+=" Error: Authorized key file does not exist or is inaccessible!\n"
return False
for d in dirA:
a = self.__write_group_other_test(d)
for entry in a:
if (entry['value']):
result = False
self.error_message+=" Error: "+entry['name']+ " permission on " + d +" is bad!\n"
a = self.__read_user_test(d)
for entry in a:
if (entry['value']):
result = False
self.error_message+=" Error: "+entry['name']+ " permission on " + d +" is bad!\n"
# test owner and perm on ~/.ssh/authorized_keys
r = self.__authorized_keys_test(keyfile)
if (r):
result = False
self.error_message+=" Error: The permission and/or ownership on " + keyfile +" is bad!\n"
return result
def execute(self):
host = syshost()
if host!="stampede" and host!="frontera":
return True
userid=getpass.getuser()
grepcmd1="""awk '/ALL = /,/ALL = /' /etc/slurm/tacc_filter_options | awk '{print substr($0,7,length($0)-7)}' | awk -v user=%s 'BEGIN {FS=" !!"}; {for (i=1; i<=NF; i++) if($i == user) {print $0}}'""" %userid
# print(grepcmd1)
myrecord1=capture(grepcmd1).split('\n')
# print(myrecord1)
grepcmd2="""awk '($1=="largemem")' /etc/slurm/tacc_filter_options | awk '{gsub(/ /, "", $0);print substr($0,12, length($0)-12)}' | awk -v user=%s 'BEGIN {FS="!!"}; {for (i=1; i<=NF; i++) if ($i == user) {print $0}}'""" %userid
# print(grepcmd2)
myrecord2=capture(grepcmd2).split('\n')
# print(myrecord2)
# grepcmd3="""awk '($1=="normal-mic" || $1=="normal-2mic")' /etc/slurm/tacc_filter_options | awk '{gsub(/ /, "", $0); print substr($0,14, length($0)-14)}' | awk -v user=%s 'BEGIN {FS="!!"}; {for (i=1; i<=NF; i++) if ($i == user) {print $0}}'""" %userid
# print(grepcmd3)
# myrecord3=capture(grepcmd3).split('\n')
# print(myrecord3)
myrecord=myrecord1 + myrecord2
# print(myrecord)
for ss in myrecord1:
if ss and not ss.strip().startswith('#'):
self.error_message+=" ERROR: You are blocked from general submission.\n"
return False
for ss in myrecord2:
if ss and not ss.strip().startswith('#'):
self.error_message+=" ERROR: You are blocked from largemem queue submission.\n"
return False
# for ss in myrecord3:
# if ss and not ss.strip().startswith('#'):
# self.error_message+=" ERROR: You are blocked from mic queue submission.\n"
# return False
return True
def execute(self):
compilers=["gcc","g++","gfortran","icc","icpc","ifort","mpicc","mpicxx","mpif90"]
Flag=True
for compiler1 in compilers:
typecmd="type %s" %compiler1
output=capture(typecmd)
if "not found" in output:
Flag=False
self.error_message+=" ERROR: Compiler %s is not available now!\n" %compiler1
return Flag
def execute(self):
host = syshost()
if host!="stampede":
return True
userid=capture("whoami").rstrip()
grepcmd1="""awk '/ALL = /,/ALL = /' /etc/slurm/tacc_filter_options | awk '{print substr($0,7,length($0)-7)}' | awk -v user=%s 'BEGIN {FS=" !!"}; {for (i=1; i<=NF; i++) if($i == user) {print $0}}'""" %userid
# print(grepcmd1)
myrecord1=capture(grepcmd1).split('\n')
# print(myrecord1)
grepcmd2="""awk '($1=="largemem")' /etc/slurm/tacc_filter_options | awk '{gsub(/ /, "", $0);print substr($0,12, length($0)-12)}' | awk -v user=%s 'BEGIN {FS="!!"}; {for (i=1; i<=NF; i++) if ($i == user) {print $0}}'""" %userid
# print(grepcmd2)
myrecord2=capture(grepcmd2).split('\n')
# print(myrecord2)
grepcmd3="""awk '($1=="normal-mic" || $1=="normal-2mic")' /etc/slurm/tacc_filter_options | awk '{gsub(/ /, "", $0); print substr($0,14, length($0)-14)}' | awk -v user=%s 'BEGIN {FS="!!"}; {for (i=1; i<=NF; i++) if ($i == user) {print $0}}'""" %userid
# print(grepcmd3)
myrecord3=capture(grepcmd3).split('\n')
# print(myrecord3)
myrecord=myrecord1 + myrecord2 + myrecord3
# print(myrecord)
for ss in myrecord1:
if ss and not ss.strip().startswith('#'):
self.error_message+="\tError: You are blocked from general submission.\n"
return False
for ss in myrecord2:
if ss and not ss.strip().startswith('#'):
self.error_message+="\tError: You are blocked from largemem queue submission.\n"
return False
for ss in myrecord3:
if ss and not ss.strip().startswith('#'):
self.error_message+="\tError: You are blocked from mic queue submission.\n"
return False
return True
def execute(self):
result = True
# home = os.environ['HOME']
userid = capture("whoami").rstrip()
# grepcmd="grep %s /etc/passwd | cut -d ':' -f6" %userid
grepcmd = "/bin/awk -F: -v user=%s '$1 == user {print $6}' </etc/passwd" % userid
home = capture(grepcmd)
if not home:
self.error_message += " ERROR: Can not find your home directory!\n"
return False
home = home[:-1]
sshD = os.path.join(home, ".ssh")
dirA = [home, sshD]
if not os.path.isdir(sshD):
self.error_message += " ERROR: No .ssh directory is found!\n"
return False
keyfile = os.path.join(sshD, "authorized_keys")
if not os.path.isfile(keyfile):
self.error_message += " ERROR: No authorized key files is found!\n"
return False
for d in dirA:
a = self.__write_group_other_test(d)
for entry in a:
if (entry['value']):
result = False
self.error_message += " ERROR: " + entry[
'name'] + " permission on " + d + " is bad!\n"
# test owner and perm on ~/.ssh/authorized_keys
r = self.__authorized_keys_test(keyfile)
if (r):
result = False
self.error_message += " ERROR: The permission and/or ownership on " + keyfile + " is bad!\n"
return result
def execute(self):
compilers=["gcc","g++","gfortran","icc","icpc","ifort","mpicc","mpicxx","mpif90"]
Flag=True
for compiler1 in compilers:
typecmd="type %s" %compiler1
output=capture(typecmd)
# print(output)
if "not found" in output:
Flag=False
self.error_message+="\tError: Compiler %s is not available at this time!\n" %compiler1
return Flag
def cleanup(xaltobj, fn):
f = open(fn,"r")
lines = f.readlines()
d = {}
for s in lines:
# remove lines with ':'
if (s.find(":") != -1):
continue
# remove line with the xalt.o file
if (s.find(xaltobj) != -1):
continue
# remove a file that is something like: /tmp/ccT33qQt.o
m = tmpObjPat.search(s)
if (m):
continue
# Capture the library name in the parens:
# -lgcc_s (/usr/lib/gcc/x86_64-linux-gnu/4.8/libgcc_s.so)
m = parenPat.search(s)
if (m):
s = os.path.realpath(m.group(1))
d[s] = True
continue
# Save everything else
idx = s.find("\n")
if (idx != -1):
s = s[:idx]
s = os.path.realpath(s)
d[s] = True
# make the list unique
sA = d.keys()
sA = sorted(sA)
sB = []
for lib in sA:
hash_line = capture(['sha1sum', lib])
if (hash_line.find("No such file or directory") != -1):
continue
else:
v = hash_line.split()[0]
sB.append([lib, v])
return sB
def execute(self):
compilers=["gcc","g++","gfortran","icc","icpc","ifort","mpicc","mpicxx","mpif90"]
Flag=True
for compiler1 in compilers:
typecmd="type %s" %compiler1
output=capture(typecmd)
# print(output)
if "not found" in output:
print("\033[1;33m\tWarning: %s is not available right now.\033[0m" %compiler1)
# Flag=False
# self.error_message+="\tError: Compiler %s is not available at this time!\n" %compiler1
return Flag
def execute(self):
host=syshost()
if host=="stampede":
commands=["sbatch","squeue","scancel"]
elif host=="ls4":
commands=["qsub","qstat","qdel"]
else:
return True
Flag=True
for command1 in commands:
typecmd="type %s" %command1
output=capture(typecmd)
if "not found" in output:
Flag=False
self.error_message+=" ERROR: Scheduler command \"%s\" is not available now!\n" %command1
return Flag
def execute(self):
host=syshost()
if host=="stampede":
commands=["sbatch","squeue","scancel"]
elif host=="ls4":
commands=["qsub","qstat","qdel"]
else:
return True
Flag=True
for command1 in commands:
typecmd="type %s" %command1
output=capture(typecmd)
if "not found" in output:
Flag=False
self.error_message+=" Error: Scheduler command \"%s\" is not available now!\n" %command1
return Flag
def execute(self):
host = syshost()
if (host == "stampede" or host == "maverick" or host == "ls5"):
commands = ["sbatch", "squeue", "scancel", "scontrol"]
elif host == "ls4":
commands = ["qsub", "qstat", "qdel"]
else:
return True
Flag = True
for command1 in commands:
typecmd = "type %s" % command1
output = capture(typecmd)
if "not found" in output:
Flag = False
self.error_message += "\tError: Scheduler command \"%s\" is not available at this time!\n" % command1
return Flag
def main():
args = CmdLineOptions().execute()
xalt = XALTdb(ConfigFn)
num = int(capture("getent passwd | wc -l"))
pbar = ProgressBar(maxVal=num)
icnt = 0
t1 = time.time()
rmapT = Rmap(args.rmapD).reverseMapT()
iuser = 0
lnkCnt = 0
runCnt = 0
for user, hdir in passwd_generator():
xaltDir = os.path.join(hdir, ".xalt.d")
if (os.path.isdir(xaltDir)):
iuser += 1
linkFnA = files_in_tree(xaltDir, "*/link.*.json")
lnkCnt += link_json_to_db(xalt, user, rmapT, linkFnA)
if (args.delete):
remove_files(linkFnA)
remove_files(files_in_tree(xaltDir, "*/.link.*.json"))
runFnA = files_in_tree(xaltDir, "*/run.*.json")
runCnt += run_json_to_db(xalt, user, rmapT, runFnA)
if (args.delete):
remove_files(runFnA)
remove_files(files_in_tree(xaltDir, "*/.run.*.json"))
icnt += 1
pbar.update(icnt)
xalt.connect().close()
pbar.fini()
t2 = time.time()
rt = t2 - t1
if (args.timer):
print("Time: ", time.strftime("%T", time.gmtime(rt)))
print("num users: ", iuser, ", num links: ", lnkCnt, ", num runs: ",
runCnt)
def main():
args = CmdLineOptions().execute()
xalt = XALTdb(ConfigFn)
num = int(capture("getent passwd | wc -l"))
pbar = ProgressBar(maxVal=num)
icnt = 0
t1 = time.time()
rmapT = Rmap(args.rmapD).reverseMapT()
iuser = 0
lnkCnt = 0
runCnt = 0
for user, hdir in passwd_generator():
xaltDir = os.path.join(hdir,".xalt.d")
if (os.path.isdir(xaltDir)):
iuser += 1
linkFnA = files_in_tree(xaltDir, "*/link.*.json")
lnkCnt += link_json_to_db(xalt, user, rmapT, linkFnA)
if (args.delete):
remove_files(linkFnA)
remove_files(files_in_tree(xaltDir, "*/.link.*.json"))
runFnA = files_in_tree(xaltDir, "*/run.*.json")
runCnt += run_json_to_db(xalt, user, rmapT, runFnA)
if (args.delete):
remove_files(runFnA)
remove_files(files_in_tree(xaltDir, "*/.run.*.json"))
icnt += 1
pbar.update(icnt)
xalt.connect().close()
pbar.fini()
t2 = time.time()
rt = t2 - t1
if (args.timer):
print("Time: ", time.strftime("%T", time.gmtime(rt)))
print("num users: ", iuser, ", num links: ", lnkCnt, ", num runs: ", runCnt)
def __build_fieldT(self, cmd):
outStr = capture(["objdump", "-s", "-j", ".xalt", cmd])
fieldT = {}
if (not outStr.find("Contents of section .xalt:") != -1):
return fieldT
outputA = outStr.split('\n')
outputA.pop(0)
outputA.pop(0)
outputA.pop(0)
outputA.pop(0)
sA = []
for line in outputA:
split = line.split()
if (len(split) > 0):
sA.append(split[-1])
s = "".join(sA)
xaltA = re.split('%%', s)
fieldT = {}
N = len(xaltA)
idx = -1
while (True):
idx = idx + 1
line = xaltA[idx]
if (line.find("XALT_Link_Info_End") != -1):
break
m = keyPat.search(line)
if (m):
key = m.group(1)
idx = idx + 1
value = xaltA[idx].replace("_%_%_"," ")
fieldT[key] = value
return fieldT
def __build_fieldT(self, cmd):
outStr = capture(["objdump", "-s", "-j", ".xalt", cmd])
fieldT = {}
if (not outStr.find("Contents of section .xalt:") != -1):
return fieldT
outputA = outStr.split('\n')
outputA.pop(0)
outputA.pop(0)
outputA.pop(0)
outputA.pop(0)
sA = []
for line in outputA:
split = line.split()
if (len(split) > 0):
sA.append(split[-1])
s = "".join(sA)
xaltA = re.split('%%', s)
fieldT = {}
N = len(xaltA)
idx = -1
while (True):
idx = idx + 1
line = xaltA[idx]
if (line.find("XALT_Link_Info_End") != -1):
break
m = keyPat.search(line)
if (m):
key = m.group(1)
idx = idx + 1
value = xaltA[idx].replace("_%_%_"," ")
fieldT[key] = value
return fieldT
def __parseLDD(self,ldd):
if (not ldd or ldd.find("not a dynamic executable") > 0):
return []
lineA = ldd.split('\n')
libA = []
d = {}
for line in lineA:
fieldA = line.split()
N = len(fieldA)
if (N < 1):
break
elif (N == 4):
lib = fieldA[2]
else:
lib = fieldA[0]
lib = os.path.realpath(lib)
d[lib] = True
libA = d.keys()
libA = sorted(libA)
libB = []
for lib in libA:
hash_line = capture(['sha1sum', lib])
if (hash_line.find("No such file or directory") != -1):
v = "unknown"
else:
v = hash_line.split()[0]
libB.append([lib, v])
return libB
def diskquota():
# primitive argument input for userid - no error checking
if len(sys.argv) == 2:
userid = sys.argv[1]
else:
userid = capture("whoami").rstrip()
#userid="u6006455"
host = syshost()
grepcmd1 = "curl --data 'unid={0}' https://www.chpc.utah.edu/apps/systems/curl_post/CHPCUserQuota.php -k -s | tail -n +2".format(
userid)
myfs = capture(grepcmd1).splitlines()
goodcolor = "32m"
badcolor = "31m"
for space in myfs:
#print(space)
# if ( (host=="ls4" and space=="/home1") or (host=="maverick" and space=="/home") or (host=="ls5" and space=="/home1")):
rawinfo = space.split("\t")
#print(rawinfo)
if (rawinfo[0] == userid) or (userid in rawinfo[0]):
usage = rawinfo[1][:-4]
files = rawinfo[3]
quota = rawinfo[2][:-1]
if rawinfo[0] == userid:
fsuse = rawinfo[5][:-4]
fsmax = rawinfo[6][:-1]
#if ((fsmax != 0) and (float(fsuse)/float(fsmax) > 0.9)):
if (isinstance(fsuse, int) and isinstance(fsmax, int)):
if (float(fsuse) / float(fsmax) > 0.9):
fscolor = badcolor
else:
fscolor = goodcolor
if quota == "0":
badusage = 100
else:
badusage = int(quota)
if float(usage) > badusage:
ucolor = badcolor
umsg = "\033[1;31mare over the quota limit\033[0m"
else:
ucolor = goodcolor
umsg = "have quota limit"
if int(files) > 100000:
fcolor = badcolor
else:
fcolor = goodcolor
if rawinfo[0] == userid:
if (rawinfo[2] == "0G"):
if (files == 0):
print(
"\tIn \033[1;36m{0}\033[0m you have no quota limit, use \033[1;{2}{1} GB\033[0m"
.format("General Home Directory", usage, ucolor))
else:
print(
"\tIn \033[1;36m{0}\033[0m you have no quota limit, use \033[1;{3}{1} GB\033[0m and have \033[1;{4}{2}\033[0m files"
.format("General Home Directory", usage, files,
ucolor, fcolor))
if (fsuse != 0):
print(
"\t (total file system usage is \033[1;{2}{0} GB\033[0m out of \033[1;{2}{1} GB\033[0m)"
.format(fsuse, fsmax, fscolor))
#print("\tOn \033[1;36m{0}\033[0m you have no quota limit, use \033[1;{3}{1} GB\033[0m (total file system usage is {5} GB out of {6} GB) and have \033[1;{4}{2}\033[0m files".format(rawinfo[0],usage,files,ucolor,fcolor,fsuse,fsmax))
else:
if (files == '0'):
print(
"\tIn \033[1;36m{0}\033[0m you {4} \033[1;{3}{2} GB\033[0m and use \033[1;{3}{1} GB\033[0m"
.format("General home directory", usage, quota,
ucolor, umsg))
else:
print(
"\tIn \033[1;36m{0}\033[0m you {6} \033[1;{4}{3} GB\033[0m, use \033[1;{4}{1} GB\033[0m and have \033[1;{5}{2}\033[0m files"
.format("General home directory", usage, files,
quota, ucolor, fcolor, umsg))
if (fsuse != '0'):
print(
"\t (total file system usage is \033[1;{2}{0} GB\033[0m out of \033[1;{2}{1} GB\033[0m)"
.format(fsuse, fsmax, fscolor))
else:
print(
"\tIn \033[1;36m{0}\033[0m you {6} \033[1;{7}{3} GB\033[0m, use \033[1;{4}{1} GB\033[0m and have \033[1;{5}{2}\033[0m files"
.format("PE Home Directory", usage, files, quota, ucolor,
fcolor, umsg, ucolor))
def execute(self):
userid=capture("whoami").rstrip()
### userid="jkatzene" #Fake test
host=syshost()
if (host=="stampede" or host=="maverick" or host=="ls5"):
TACC_ACC_DIR="/usr/local/etc/"
elif host=="ls4":
TACC_ACC_DIR="/sge_common/default/acct/map/"
else:
return True
proj_map=TACC_ACC_DIR+"project.map"
projuser_map=TACC_ACC_DIR+"projectuser.map"
projbalance_map=TACC_ACC_DIR+"projectbalance.map"
usage_map=TACC_ACC_DIR+"usage.map"
# grepcmd="grep %s %s" %(userid,projuser_map)
grepcmd="""awk -v user=%s '$1 == user {print $0}' %s """ %(userid,projuser_map)
# print(grepcmd)
myprojects=capture(grepcmd).split()
# print(myprojects)
if len(myprojects) < 2:
self.error_message+="\tError: "+"No valid allocation\n"
return False
Flag=False
for proj in myprojects[1:]:
grepcmd="grep %s$ %s" %(proj,proj_map)
# print(grepcmd)
proj_name_all=capture(grepcmd).split()
# print(proj_name_all)
if proj_name_all:
proj_name=proj_name_all[0]
# grepcmd="grep %s %s" %(proj_name,usage_map)
grepcmd="awk -F: '{ if ($1==\"%s\") print}' %s" %(proj_name,usage_map)
# print(grepcmd)
# print(capture(grepcmd))
usage_report=capture(grepcmd).split(":")
if len(usage_report) < 6:
print("\033[1;33m\tWarning: Valid allocation detected.\033[0m")
continue
exp_date=usage_report[3].split("-")
exp_date_f=date(int(exp_date[0]), int(exp_date[1]), int(exp_date[2]))
today = date.today()
cur_bal=float(usage_report[6])
# print(" My project '%s'; balance %s." %(proj_name,cur_bal))
if exp_date_f < date.today():
print("\033[1;33m\tWarning: One of your projects '%s' has expired.\033[0m" %proj_name[0])
elif cur_bal < 0:
print("\033[1;33m\tWarning: One of your projects '%s' has negative balance %s.\033[0m" %(proj_name,cur_bal))
else:
Flag=True
if Flag:
return True
else:
self.error_message+="\tError: All your allocations are invalid"
return Flag
def _capture(self,cmd):
return capture(self._cmd(cmd))
def __computeHash(self, cmd): fieldA = capture(["sha1sum", cmd]).split() return fieldA[0]
def main():
try:
uuid = sys.argv[ 1]
status = sys.argv[ 2]
wd = sys.argv[ 3]
syshost = sys.argv[ 4]
pstree = sys.argv[ 5]
execname = sys.argv[ 6]
xaltobj = sys.argv[ 7]
build_epoch = sys.argv[ 8]
linklineFn = sys.argv[ 9]
resultFn = sys.argv[10]
if (execname.find("conftest") != -1):
return 1
hash_line = capture(['sha1sum', execname])
if (hash_line.find("No such file or directory") != -1):
return 1
hash_id = hash_line.split()[0]
# Step one clean up linkline data
sA = cleanup(xaltobj, linklineFn)
resultT = {}
resultT['uuid'] = uuid
resultT['link_program'] = extract_compiler(pstree)
resultT['build_user'] = os.environ['USER']
resultT['exit_code'] = status
resultT['build_epoch'] = build_epoch
resultT['exec_path'] = os.path.abspath(execname)
resultT['hash_id'] = hash_id
resultT['wd'] = wd
resultT['build_syshost'] = syshost
resultT['linkA'] = sA
dirname,fn = os.path.split(resultFn)
tmpFn = os.path.join(dirname, "." + fn)
except:
logger.exception("XALT_EXCEPTION:xalt_generate_linkdata")
try:
if (not os.path.isdir(dirname)):
os.mkdir(dirname);
s = json.dumps(resultT, sort_keys=True, indent=2, separators=(',',': '))
f = open(tmpFn,'w')
f.write(s)
f.write("\n")
if (hash_line.find("sha1sum:") != -1):
f.write(hash_line)
f.close()
os.rename(tmpFn, resultFn)
except (OSError):
logger.exception("XALT_EXCEPTION:xalt_generate_linkdata(write json file)")
return 0
def __computeHash(self, cmd): fieldA = capture(["sha1sum", cmd]).split() return fieldA[0]
def allocations():
host = syshost()
#print(host)
if (host!="kingspeak")and(host!="ember")and(host!="lonepeak")and(host!="notchpeak")and(host!="ash")and(host!="redwood")and(host!="crystalpeak"):
print("This command needs to run on one of the CHPC clusters")
sys.exit(1)
# primitive argument input for userid - no error checking
if len(sys.argv)==2:
userid=sys.argv[1]
else:
userid=capture("whoami").rstrip()
#userid="u1119546"
#userid="u0631741"
# redwood tests
#userid="u6000771"
#userid="u0413537"
#userid="u6002243"
# MC Jan 20
# potentially cleaner version may be to create a list of account-QOS associations with sacctmgr
# and then compare QOS from each of the association to the "scontrol -o show partition" output to get the corresponding partition
# the scontrol can be run only once with result stored in an array so that it's not run repeatedly
# sacctmgr -p show qos lists what QOSes can this one preempt (Preempt = column 4), can see if preemptable QOS is in this output which would mean that it's preemptable
grepcmd1="sacctmgr -n -p show assoc where user={0}".format(userid)
#print(grepcmd1)
myaccts=capture(grepcmd1).split()
#print(myaccts,len(myaccts))
if host=="redwood":
clusters=["redwood"]
elif host=="crystalpeak":
clusters=["crystalpeak"]
else:
clusters=["kingspeak","notchpeak","lonepeak","ash"]
for cluster in clusters:
FCFlag=True
if cluster=="kingspeak":
cl="kp"
elif cluster=="notchpeak":
cl="np"
elif cluster=="ember":
cl="em"
elif cluster=="lonepeak":
cl="lp"
elif cluster=="ash":
cl="smithp-ash"
elif cluster=="redwood":
cl="rw"
elif cluster=="crystalpeak":
cl="cp"
matchcl = [s for s in myaccts if cluster in s]
#print(matchcl, len(matchcl))
if len(matchcl) > 0:
if (len(matchcl) > 1):
# first filter out owner accounts
# this will be true if there are owner nodes
matchstr="^((?!-{0}).)*$".format(cl)
#print(matchstr)
r=re.compile(matchstr)
matchcl = list(filter(r.match, matchcl))
#print(matchcl)
#print("Error, more than 1 match: {0}".format(matchcl))
# now filter out the freecycle accounts
matchfc = [s for s in matchcl if "freecycle" in s]
if len(matchfc) > 0:
#print(matchfc)
for matchfc0 in matchfc:
pnames=matchfc0.split('|')
#print(pnames)
print("\tYour group \033[1;31m{0}\033[0m does not have a \033[1;36mgeneral\033[0m allocation on \033[1;34m{1}\033[0m".format(pnames[1],cluster))
print("\tYou can use \033[1;33mpreemptable\033[0m mode on \033[1;34m{0}\033[0m. Account: \033[1;32m{1}\033[0m, Partition: \033[1;32m{2}\033[0m".format(cluster,pnames[1],pnames[17]))
print("\tYou can use \033[1;33mpreemptable\033[0m mode on \033[1;34m{0}\033[0m. Account: \033[1;32m{1}\033[0m, Partition: \033[1;32m{2}\033[0m".format(cluster,pnames[1],cluster+"-shared-freecycle"))
# now look at allocated group accounts - so need to exclude owner-guest and freecycle
matchg1 = [s for s in matchcl if not "freecycle" in s]
#print(matchg1)
matchg2 = [s for s in matchg1 if not "guest" in s]
matchg3 = [s for s in matchg2 if not "collab" in s]
# also filter out gpu accounts
matchg4 = [s for s in matchg3 if not "gpu" in s]
#matchg = [s for s in matchg2 if not "shared-short" in s]
matchg = [s for s in matchg4 if not "notchpeak-shared" in s]
if len(matchg)>0:
#print(matchg)
for matchg1 in matchg:
#print(matchg1)
myrecord1 = matchg1.split('|')
#print(myrecord1)
print("\tYou have a \033[1;36mgeneral\033[0m allocation on \033[1;34m{1}\033[0m. Account: \033[1;32m{0}\033[0m, Partition: \033[1;32m{2}\033[0m".format(myrecord1[1],cluster,myrecord1[18]))
if (myrecord1[1] != "dtn"): # account dtn that matches here does not have shared partition
print("\tYou have a \033[1;36mgeneral\033[0m allocation on \033[1;34m{1}\033[0m. Account: \033[1;32m{0}\033[0m, Partition: \033[1;32m{2}\033[0m".format(myrecord1[1],cluster,cluster+"-shared"))
# shared-short
matchgrp = [s for s in myaccts if "shared-short" in s]
matchcl = [s for s in matchgrp if cluster in s]
if len(matchcl) > 0:
matchstr="^((?!{0}).)*$".format(cl)
r=re.compile(matchstr)
matchcl = list(filter(r.match, matchcl))
pnames=matchcl[0].split('|')
print("\tYou have a \033[1;36mgeneral\033[0m allocation on \033[1;34m{0}\033[0m. Account: \033[1;32m{1}\033[0m, Partition: \033[1;32m{1}\033[0m".format(cluster,pnames[1]))
# owner accounts
grepcmd1="sacctmgr -p show assoc where user={0} | grep {1} | grep -w {2} | grep -v guest".format(userid,cluster,cl) # need to grep out guest since for ash cl=smithp-ash
#print(grepcmd1)
myprojects=capture(grepcmd1).split()
#print(myprojects,len(myprojects))
if len(myprojects) > 0:
for project in myprojects:
pnames=project.split('|')
#print(pnames)
# MC 1/24/20 - using scontrol to grep for partition that corresponds to the QOS in pnames[18]
# example user that had QOS vs partition mix up - u6022494
qosname = pnames[18]
# in case "Def QOS" = pnames[18] is not defined, try "QOS" = pnames[17]
if len(pnames[18]) == 0:
qosname = pnames[17]
grepcmd2="scontrol -M {1} -o show partition | grep {0} | grep -v shared".format(qosname,cluster)
#print(grepcmd2)
myparts=capture(grepcmd2).split()
if len(myparts) > 0:
#print(myparts,len(myparts))
#print(myparts[0])
mypart=myparts[0].split('=')
#print(mypart[1])
pgroup=mypart[1].split('-')
print("\tYou have an \033[1;36mowner\033[0m allocation on \033[1;34m{0}\033[0m. Account: \033[1;32m{1}\033[0m, Partition: \033[1;32m{2}\033[0m".format(cluster,pnames[1],mypart[1]))
print("\tYou have an \033[1;36mowner\033[0m allocation on \033[1;34m{0}\033[0m. Account: \033[1;32m{1}\033[0m, Partition: \033[1;32m{2}\033[0m".format(cluster,pnames[1],pgroup[0]+"-shared-"+pgroup[1]))
else:
print("\t\033[1;31mError:\033[0m you are in QOS \033[1;34m{0}\033[0m, but partition \033[1;32m{0}\033[0m does not exist. Please contact CHPC to fix this.".format(qosname))
# collab accounts
grepcmd1="sacctmgr -p show assoc where user={0} | grep {1} | grep -w {2} | grep -v guest".format(userid,cluster,"collab") # need to grep out guest since for ash cl=smithp-ash
#print(grepcmd1)
myprojects=capture(grepcmd1).split()
#print(myprojects,len(myprojects))
if len(myprojects) > 0:
for project in myprojects:
pnames=project.split('|')
pgroup=pnames[17].split('-')
#print(pnames)
print("\tYou have an \033[1;36mowner\033[0m allocation on \033[1;34m{0}\033[0m. Account: \033[1;32m{1}\033[0m, Partition: \033[1;32m{2}\033[0m".format(cluster,pnames[1],pgroup[0]+"-"+cl))
print("\tYou have an \033[1;36mowner\033[0m allocation on \033[1;34m{0}\033[0m. Account: \033[1;32m{1}\033[0m, Partition: \033[1;32m{2}\033[0m".format(cluster,pnames[1],pgroup[0]+"-shared-"+cl))
# owner guest
# have to get matchcl again since we may have changed it above
matchcl = [s for s in myaccts if cluster in s]
matchstr=".*\\bguest\\.*"
#print(matchstr)
#print(matchcl, len(matchcl))
r=re.compile(matchstr)
myprojects = list(filter(r.match, matchcl))
#print(myprojects)
if len(myprojects) > 0:
for project in myprojects:
if "gpu" in project:
gpustr = " GPU"
else:
gpustr = ""
pnames=project.split('|')
part=pnames[17].split(',')
# #print(pnames)
print("\tYou can use \033[1;33mpreemptable{3}\033[0m mode on \033[1;34m{0}\033[0m. Account: \033[1;32m{1}\033[0m, Partition: \033[1;32m{2}\033[0m".format(cluster,pnames[1],part[0],gpustr))
# GPU accounts
grepcmd1="sacctmgr -p show assoc where user={0} | grep {1} | grep -w gpu | grep -v guest".format(userid,cluster)
#print(grepcmd1)
myprojects=capture(grepcmd1).split()
if len(myprojects) > 0:
for project in myprojects:
pnames=project.split('|')
#print(pnames)
print("\tYou have a \033[1;36mGPU\033[0m allocation on \033[1;34m{0}\033[0m. Account: \033[1;32m{1}\033[0m, Partition: \033[1;32m{2}\033[0m".format(cluster,pnames[1],pnames[17]))
