Python subprocess.PIPE Examples

The following are 30 code examples of subprocess.PIPE(). You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may also want to check out all available functions/classes of the module subprocess , or try the search function .
Example #1
Source File: test.py    From aegea with Apache License 2.0 16 votes vote down vote up
def call(self, cmd, **kwargs):
        print('Running "{}"'.format(cmd), file=sys.stderr)
        expect = kwargs.pop("expect", [dict(return_codes=[os.EX_OK], stdout=None, stderr=None)])
        process = subprocess.Popen(cmd, stdin=kwargs.get("stdin", subprocess.PIPE), stdout=subprocess.PIPE,
                                   stderr=subprocess.PIPE, **kwargs)
        out, err = process.communicate()
        return_code = process.poll()
        out = out.decode(sys.stdin.encoding)
        err = err.decode(sys.stdin.encoding)

        def match(return_code, out, err, expected):
            exit_ok = return_code in expected["return_codes"]
            stdout_ok = re.search(expected.get("stdout") or "", out)
            stderr_ok = re.search(expected.get("stderr") or "", err)
            return exit_ok and stdout_ok and stderr_ok
        if not any(match(return_code, out, err, exp) for exp in expect):
            print(err)
            e = subprocess.CalledProcessError(return_code, cmd, output=out)
            e.stdout, e.stderr = out, err
            raise e
        return self.SubprocessResult(out, err, return_code) 
Example #2
Source File: core.py    From BASS with GNU General Public License v2.0 9 votes vote down vote up
def get_num_triggering_samples(signature, samples):
    """
        Get number of samples triggering ClamAV signature _signature_.
        :param signature: A dictionary with keys 'type' for the signature type
            and 'signature' for the signature string.
        :param samples: A list of sample paths to scan.
        :returns: The number of samples triggering this signature.
    """
    handle, temp_sig = tempfile.mkstemp(suffix = "." + signature["type"])
    try:
        with os.fdopen(handle, "w") as f:
            f.write(signature["signature"])
        proc_clamscan = subprocess.Popen(["clamscan", 
                                          "-d", temp_sig,
                                          "--no-summary", "--infected"] + samples, 
                                         stdout = subprocess.PIPE,
                                         stderr = subprocess.PIPE)
        stdout, stderr = proc_clamscan.communicate()
        if not stdout:
            return 0
        else:
            return len(stdout.strip().split("\n"))
    finally:
        os.unlink(temp_sig) 
Example #3
Source File: inst.py    From kaldi-python-io with Apache License 2.0 9 votes vote down vote up
def pipe_fopen(command, mode, background=True):
    if mode not in ["rb", "r"]:
        raise RuntimeError("Now only support input from pipe")

    p = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)

    def background_command_waiter(command, p):
        p.wait()
        if p.returncode != 0:
            warnings.warn("Command \"{0}\" exited with status {1}".format(
                command, p.returncode))
            _thread.interrupt_main()

    if background:
        thread = threading.Thread(target=background_command_waiter,
                                  args=(command, p))
        # exits abnormally if main thread is terminated .
        thread.daemon = True
        thread.start()
    else:
        background_command_waiter(command, p)
    return p.stdout 
Example #4
Source File: alignproc.py    From svviz with MIT License 8 votes vote down vote up
def alignProcWrapper(ref, seq):
    cmd = "python {} {} {}".format(
        os.path.realpath(__file__),
        ref,
        seq)
    
    proc = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    out, err = proc.communicate()

    if proc.returncode != 0:
        return None

    fields = out.split()
    strand = fields[0].decode()
    
    aln = Aln(int(fields[1]), int(fields[2]), fields[3].decode(), int(fields[4]), int(fields[5]))

    return strand, aln 
Example #5
Source File: sifter.py    From sandsifter with BSD 3-Clause "New" or "Revised" License 8 votes vote down vote up
def disas_objdump(b):
    with open("/dev/shm/shifter", "w") as f:
        f.write(b)
    if arch == "64":
        dis, errors = subprocess.Popen("objdump -D --insn-width=256 -b binary \
                -mi386 -Mx86-64 /dev/shm/shifter | head -8 | tail -1",
                stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True).communicate()
    else:
        dis, errors = subprocess.Popen("objdump -D --insn-width=256 -b binary \
                -mi386 /dev/shm/shifter | head -8 | tail -1",
                stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True).communicate()
    dis = dis[6:] # address
    raw = dis[:256*3].replace(" ","")
    dis = dis[256*3:].strip().split(None, 2)
    mnemonic = dis[0]
    if len(dis) > 1:
        op_str = dis[1]
    else:
        op_str = ""
    if mnemonic == "(bad)":
        mnemonic = "(unk)"
        insn = ""
        op_str = ""
    size = len(raw)/2
    return (mnemonic, op_str, size) 
Example #6
Source File: setup.py    From EDeN with MIT License 7 votes vote down vote up
def update_version_py():
    if not os.path.isdir(".git"):
        print("This does not appear to be a Git repository.")
        return
    try:
        # p = subprocess.Popen(["git", "describe","--tags", "--always"],
        #        stdout=subprocess.PIPE)
        p = subprocess.Popen("git rev-list HEAD --count".split(),
                             stdout=subprocess.PIPE)

    except EnvironmentError:
        print("unable to run git, leaving eden/_version.py alone")
        return
    stdout = p.communicate()[0]
    if p.returncode != 0:
        print("unable to run git, leaving eden/_version.py alone")
        return
    ver = "0.3."+stdout.strip()
    # ver = str(int(ver,16)) # pypi doesnt like base 16
    f = open("eden/_version.py", "w")
    f.write(VERSION_PY % ver)
    f.close()
    print("set eden/_version.py to '%s'" % ver) 
Example #7
Source File: straight_dope_test_utils.py    From dynamic-training-with-apache-mxnet-on-aws with Apache License 2.0 7 votes vote down vote up
def _run_command(cmd, timeout_secs=300):
    """ Runs a command with a specified timeout.

    Args:
        cmd : list of string
            The command with arguments to run.
        timeout_secs: integer
            The timeout in seconds

    Returns:
        Returns the process and the output as a pair.
    """
    proc = subprocess.Popen(
        cmd,
        stdout=subprocess.PIPE,
        stderr=subprocess.STDOUT)

    for i in range(timeout_secs):
        sleep(1)
        if proc.poll() is not None:
            (out, _) = proc.communicate()
            return proc, out.decode('utf-8')

    proc.kill()
    return proc, "Timeout of %s secs exceeded." % timeout_secs 
Example #8
Source File: osdriver.py    From multibootusb with GNU General Public License v2.0 7 votes vote down vote up
def dd_iso_image(self, input_, output, gui_update, status_update):
        ''' Implementation for OS that use dd to write the iso image. 
        '''
        in_file_size = os.path.getsize(input_)
        cmd = [self.dd_exe, 'if=' + input_,
               'of=' + self.physical_disk(output), 'bs=1M']
        self.dd_iso_image_add_args(cmd, input_, output)
        kw_args = {
            'stdout' : subprocess.PIPE,
            'stderr' : subprocess.PIPE,
            'shell'  : False,
            }
        self.add_dd_iso_image_popen_args(kw_args)
        self.dd_iso_image_prepare(input, output, status_update)
        log('Executing => ' + str(cmd))
        dd_process = subprocess.Popen(cmd, **kw_args)
        output_q = queue.Queue()
        while dd_process.poll() is None:
            self.dd_iso_image_readoutput(dd_process, gui_update, in_file_size,
                                         output_q)
        output_lines = [output_q.get() for i in range(output_q.qsize())]
        for l in output_lines:
            log('dd: ' + l)
        return self.dd_iso_image_interpret_result(
            dd_process.returncode, output_lines) 
Example #9
Source File: calcs.py    From mlearn with BSD 3-Clause "New" or "Revised" License 6 votes vote down vote up
def calculate(self):
        """
        Calculate the vacancy formation given Potential class.
        """
        with ScratchDir('.'):
            input_file, energy_per_atom, num_atoms = self._setup()
            p = subprocess.Popen([self.LMP_EXE, '-in', input_file], stdout=subprocess.PIPE)
            stdout = p.communicate()[0]

            rc = p.returncode
            if rc != 0:
                error_msg = 'LAMMPS exited with return code %d' % rc
                msg = stdout.decode("utf-8").split('\n')[:-1]
                try:
                    error_line = [i for i, m in enumerate(msg)
                                  if m.startswith('ERROR')][0]
                    error_msg += ', '.join([e for e in msg[error_line:]])
                except Exception:
                    error_msg += msg[-1]
                raise RuntimeError(error_msg)
            defect_energy, _, _ = self._parse()
        defect_formation_energy = defect_energy - energy_per_atom * num_atoms

        return defect_formation_energy 
Example #10
Source File: export.py    From svviz with MIT License 6 votes vote down vote up
def checkInkscape():
    try:
        subprocess.check_call("inkscape --version", stdout=subprocess.PIPE, shell=True)
        return True
    except subprocess.CalledProcessError:
        return False 
Example #11
Source File: interface.py    From XFLTReaT with MIT License 6 votes vote down vote up
def win_set_intermediate_route(self, serverip, proxyip):
		common.internal_print("Changing route table for intermediate hop")
		# delete original default route
		ps = subprocess.Popen(["route", "DELETE", serverip, self.orig_default_gw], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
		(stdout, stderr) = ps.communicate()
		if stderr:
			common.internal_print("Delete server route failed: {0}".format(stderr), -1)
			sys.exit(-1)

		# add intermediate route
		ps = subprocess.Popen(["route", "ADD", proxyip, "MASK", "255.255.255.255", self.orig_default_gw], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
		(stdout, stderr) = ps.communicate()
		if stderr:
			common.internal_print("Add intermediate route failed: {0}".format(stderr), -1)
			sys.exit(-1)

		return 
Example #12
Source File: interface.py    From XFLTReaT with MIT License 6 votes vote down vote up
def win_restore_routes(self, serverip, clientip, ip):
		common.internal_print("Restoring default route")

		ps = subprocess.Popen(["route", "DELETE", serverip, self.orig_default_gw], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
		(stdout, stderr) = ps.communicate()
		if stderr:
			common.internal_print("Delete server route failed: {0}".format(stderr), -1)
			sys.exit(-1)

		ps = subprocess.Popen(["route", "-p", "DELETE", "0.0.0.0", ip], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
		(stdout, stderr) = ps.communicate()
		if stderr:
			common.internal_print("Delete default route failed: {0}".format(stderr), -1)
			sys.exit(-1)

		ps = subprocess.Popen(["route", "ADD", "0.0.0.0", "MASK", "0.0.0.0", self.orig_default_gw], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
		(stdout, stderr) = ps.communicate()
		if stderr:
			common.internal_print("Add original default route failed: {0}".format(stderr), -1)
			sys.exit(-1)

		return 
Example #13
Source File: interface.py    From XFLTReaT with MIT License 6 votes vote down vote up
def mac_set_ip_address(self, dev, ip, serverip, netmask):
		ifr = struct.pack('<16sBBHIIIBBHIIIBBHIII',
			self.iface_name,
			16, socket.AF_INET, 0, struct.unpack('<L', socket.inet_pton(socket.AF_INET, ip))[0], 0, 0,
			16, socket.AF_INET, 0, struct.unpack('<L', socket.inet_pton(socket.AF_INET, serverip))[0], 0, 0,
			16, 0, 0, struct.unpack('<L', socket.inet_pton(socket.AF_INET, "255.255.255.255"))[0], 0, 0)
		try:
			sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
			fcntl.ioctl(sock, self.IOCTL_MACOSX_SIOCAIFADDR, ifr)
		except Exception as e:
			common.internal_print("Something went wrong with setting up the interface.", -1)
			print(e)
			sys.exit(-1)

		# adding new route for forwarding packets properly.
		integer_ip = struct.unpack(">I", socket.inet_pton(socket.AF_INET, serverip))[0]
		rangeip = socket.inet_ntop(socket.AF_INET, struct.pack(">I", integer_ip & ((2**int(netmask))-1)<<32-int(netmask)))
		ps = subprocess.Popen(["route", "add", "-net", rangeip+"/"+netmask, serverip], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
		(stdout, stderr) = ps.communicate()
		if stderr:
			if not "File exists" in stderr:
				common.internal_print("Error: adding client route: {0}".format(stderr), -1)
				sys.exit(-1)

		return 
Example #14
Source File: interface.py    From XFLTReaT with MIT License 6 votes vote down vote up
def win_check_default_route(self):
		# get default gateway
		ps = subprocess.Popen(["route", "-4", "PRINT", "0.0.0.0"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
		(stdout, stderr) = ps.communicate()
		if stderr:
			common.internal_print("Checking default route failed: {0}".format(stderr), -1)
			sys.exit(-1)

		# count default routes
		default_routes = 0
		for line in stdout[0:stdout.find("Persistent Routes:")].split("\n"):
			if "0.0.0.0" in line:
				default_routes += 1

		if not default_routes:
			common.internal_print("No default route. Please set up your routing before executing the tool", -1)
			sys.exit(-1)

		return 
Example #15
Source File: interface.py    From XFLTReaT with MIT License 6 votes vote down vote up
def mac_set_intermediate_route(self, serverip, proxyip):
		common.internal_print("Changing route table for intermediate hop")

		ps = subprocess.Popen(["route", "delete", serverip, self.orig_default_gw], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
		(stdout, stderr) = ps.communicate()
		if stderr:
			common.internal_print("Error: delete old route: {0}".format(stderr), -1)
			sys.exit(-1)

		ps = subprocess.Popen(["route", "add", "-net", proxyip, self.orig_default_gw, "255.255.255.255"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
		(stdout, stderr) = ps.communicate()
		if stderr:
			if not "File exists" in stderr:
				common.internal_print("Error: adding server route: {0}".format(stderr), -1)
				sys.exit(-1)
		return 
Example #16
Source File: utils.py    From Att-ChemdNER with Apache License 2.0 6 votes vote down vote up
def get_perf(filename):
    ''' run conlleval.pl perl script to obtain
    precision/recall and F1 score '''
    _conlleval = PREFIX + 'conlleval'
    if not isfile(_conlleval):
        #download('http://www-etud.iro.umontreal.ca/~mesnilgr/atis/conlleval.pl') 
        os.system('wget https://www.comp.nus.edu.sg/%7Ekanmy/courses/practicalNLP_2008/packages/conlleval.pl')
        chmod('conlleval.pl', stat.S_IRWXU) # give the execute permissions
    
    out = []
    proc = subprocess.Popen(["perl", _conlleval], stdin=subprocess.PIPE, stdout=subprocess.PIPE)
    stdout, _ = proc.communicate(open(filename).read())
    for line in stdout.split('\n'):
        if 'accuracy' in line:
            out = line.split()
            break
    
    # out = ['accuracy:', '16.26%;', 'precision:', '0.00%;', 'recall:', '0.00%;', 'FB1:', '0.00']
    precision = float(out[3][:-2])
    recall    = float(out[5][:-2])
    f1score   = float(out[7])

    return {'p':precision, 'r':recall, 'f1':f1score} 
Example #17
Source File: interface.py    From XFLTReaT with MIT License 6 votes vote down vote up
def WIN_get_interface_index(self):
		iface_name = self.WIN_get_subinterface_name()
		ps = subprocess.Popen(["netsh", "interface", "ipv4", "show", "interfaces"], stdout=subprocess.PIPE,
			stderr=subprocess.PIPE)
		(stdout, stderr) = ps.communicate()


		if stderr != "":
			common.internal_print("Show interfaces. netsh failed: {0}".format(stdout), -1)
			sys.exit(-1)

		for line in stdout.split("\n"):
			if iface_name in line:
				i = 0
				while line[i:i+1] == " ":
					i += 1
				return int(line[i:].split(" ")[0])

		return -1 
Example #18
Source File: versioneer.py    From aospy with Apache License 2.0 6 votes vote down vote up
def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
                env=None):
    """Call the given command(s)."""
    assert isinstance(commands, list)
    p = None
    for c in commands:
        try:
            dispcmd = str([c] + args)
            # remember shell=False, so use git.cmd on windows, not just git
            p = subprocess.Popen([c] + args, cwd=cwd, env=env,
                                 stdout=subprocess.PIPE,
                                 stderr=(subprocess.PIPE if hide_stderr
                                         else None))
            break
        except EnvironmentError:
            e = sys.exc_info()[1]
            if e.errno == errno.ENOENT:
                continue
            if verbose:
                print("unable to run %s" % dispcmd)
                print(e)
            return None, None
    else:
        if verbose:
            print("unable to find command, tried %s" % (commands,))
        return None, None
    stdout = p.communicate()[0].strip()
    if sys.version_info[0] >= 3:
        stdout = stdout.decode()
    if p.returncode != 0:
        if verbose:
            print("unable to run %s (error)" % dispcmd)
            print("stdout was %s" % stdout)
        return None, p.returncode
    return stdout, p.returncode 
Example #19
Source File: interface.py    From XFLTReaT with MIT License 6 votes vote down vote up
def lin_set_intermediate_route(self, serverip, proxyip):
		common.internal_print("Changing route table for intermediate hop")
		ps = subprocess.Popen(["route", "delete", serverip, "gw", self.orig_default_gw], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
		(stdout, stderr) = ps.communicate()
		if stderr:
			common.internal_print("Error: delete old route: {0}".format(stderr), -1)
			sys.exit(-1)

		ps = subprocess.Popen(["route", "add", "-host", proxyip, "gw", self.orig_default_gw], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
		(stdout, stderr) = ps.communicate()
		if stderr:
			if not "File exists" in stderr:
				common.internal_print("Error: adding server route: {0}".format(stderr), -1)
				sys.exit(-1)

		return 
Example #20
Source File: interface.py    From XFLTReaT with MIT License 6 votes vote down vote up
def lin_check_default_route(self):
		# get default gateway(s)
		ps = subprocess.Popen(["route", "-n"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
		(stdout, stderr) = ps.communicate()

		if stderr != "":
			common.internal_print("Route error: {0}".format(stderr), -1)
			sys.exit(-1)

		lines = stdout.split("\n")
		default_route_number = 0
		for line in lines:
			if line[0:7] == "0.0.0.0":
				default_route_number += 1

		if default_route_number < 1:
			common.internal_print("No default route. Please set up your routing before executing the tool", -1)
			sys.exit(-1)
		if default_route_number > 1:
			common.internal_print("More than one default route. This should be reviewed before executing the tool.", -1)
			sys.exit(-1)

		return 
Example #21
Source File: interface.py    From XFLTReaT with MIT License 6 votes vote down vote up
def lin_set_ip_address(self, dev, ip, serverip, netmask):
		sockfd = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
		try:
			# set IP
			ifr  = struct.pack('<16sH2s4s8s', dev, socket.AF_INET, "\x00"*2, socket.inet_aton(ip), "\x00"*8)
			fcntl.ioctl(sockfd, self.IOCTL_LINUX_SIOCSIFADDR, ifr)

			# get flags
			ifr = struct.pack('<16sh', dev, 0)
			flags = struct.unpack('<16sh', fcntl.ioctl(sockfd, self.IOCTL_LINUX_SIOCSIFFLAGS, ifr))[1]

			# set new flags
			flags = flags | self.IOCTL_LINUX_IFF_UP
			ifr = struct.pack('<16sh', dev, flags)

			# iface up
			fcntl.ioctl(sockfd, self.IOCTL_LINUX_SIOCSIFFLAGS, ifr)
		except Exception as e:
			common.internal_print("Something went wrong with setting up the interface.", -1)
			print(e)
			sys.exit(-1)

		# adding new route for forwarding packets properly.
		integer_ip = struct.unpack(">I", socket.inet_pton(socket.AF_INET, serverip))[0]
		rangeip = socket.inet_ntop(socket.AF_INET, struct.pack(">I", integer_ip & ((2**int(netmask))-1)<<32-int(netmask)))

		integer_netmask = struct.pack(">I", ((2**int(netmask))-1)<<32-int(netmask))
		netmask = socket.inet_ntoa(integer_netmask)

		ps = subprocess.Popen(["route", "add", "-net", rangeip, "netmask", netmask, "dev", dev], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
		(stdout, stderr) = ps.communicate()
		if stderr:
			if not "File exists" in stderr:
				common.internal_print("Error: adding client route: {0}".format(stderr), -1)
				sys.exit(-1)

		return 
Example #22
Source File: _cpmodpy.py    From cherrypy with BSD 3-Clause "New" or "Revised" License 6 votes vote down vote up
def popen(fullcmd):
        p = subprocess.Popen(fullcmd, shell=True,
                             stdout=subprocess.PIPE, stderr=subprocess.STDOUT,
                             close_fds=True)
        return p.stdout 
Example #23
Source File: ICMP.py    From XFLTReaT with MIT License 6 votes vote down vote up
def communication_initialization(self):
		self.clients = []
		if self.serverorclient:
			if self.os_type == common.OS_LINUX:
				ps = subprocess.Popen(["cat", "/proc/sys/net/ipv4/icmp_echo_ignore_all"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
				(stdout, stderr) = ps.communicate()
				if stderr:
					common.internal_print("Error: deleting default route: {0}".format(stderr), -1)
					sys.exit(-1)
				self.orig_ieia_value = stdout[0:1]
				os.system("echo 1 > /proc/sys/net/ipv4/icmp_echo_ignore_all")

		if self.serverorclient:
			self.ICMP_send = self.icmp.ICMP_ECHO_RESPONSE
		else:
			self.ICMP_send = self.icmp.ICMP_ECHO_REQUEST
		return 
Example #24
Source File: osdriver.py    From multibootusb with GNU General Public License v2.0 6 votes vote down vote up
def gpt_device(self, dev_name):
        disk_dev = self.physical_disk(dev_name)
        cmd = ['parted', disk_dev, '-s', 'print']
        with open(os.devnull) as devnull:
            p = subprocess.Popen(cmd, stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE, stdin=devnull)
            _cmd_out, _err_out = p.communicate()
            p.wait()
        if p.returncode != 0:
            lang = os.getenv('LANG')
            encoding = lang.rsplit('.')[-1] if lang else 'utf-8'
            raise RuntimeError(str(_err_out, encoding))
        subprocess.check_call(['partprobe', disk_dev])
        if b'msdos' in _cmd_out:
            return False
        if b'gpt' in _cmd_out:
            return True
        raise RuntimeError("Disk '%s' is uninitialized and not usable." %
                           disk_dev) 
Example #25
Source File: setup.py    From mmdetection with Apache License 2.0 6 votes vote down vote up
def get_git_hash():

    def _minimal_ext_cmd(cmd):
        # construct minimal environment
        env = {}
        for k in ['SYSTEMROOT', 'PATH', 'HOME']:
            v = os.environ.get(k)
            if v is not None:
                env[k] = v
        # LANGUAGE is used on win32
        env['LANGUAGE'] = 'C'
        env['LANG'] = 'C'
        env['LC_ALL'] = 'C'
        out = subprocess.Popen(
            cmd, stdout=subprocess.PIPE, env=env).communicate()[0]
        return out

    try:
        out = _minimal_ext_cmd(['git', 'rev-parse', 'HEAD'])
        sha = out.strip().decode('ascii')
    except OSError:
        sha = 'unknown'

    return sha 
Example #26
Source File: calcs.py    From mlearn with BSD 3-Clause "New" or "Revised" License 6 votes vote down vote up
def calculate(self):
        """
        Calculate the elastic constant given Potential class.
        """
        with ScratchDir('.'):
            input_file = self._setup()
            p = subprocess.Popen([self.LMP_EXE, '-in', input_file],
                                 stdout=subprocess.PIPE)
            stdout = p.communicate()[0]
            rc = p.returncode
            if rc != 0:
                error_msg = 'LAMMPS exited with return code %d' % rc
                msg = stdout.decode("utf-8").split('\n')[:-1]
                try:
                    error_line = [i for i, m in enumerate(msg)
                                  if m.startswith('ERROR')][0]
                    error_msg += ', '.join([e for e in msg[error_line:]])
                except Exception:
                    error_msg += msg[-1]
                raise RuntimeError(error_msg)
            result = self._parse()
        return result 
Example #27
Source File: sifter.py    From sandsifter with BSD 3-Clause "New" or "Revised" License 6 votes vote down vote up
def start(self):
        self.command = "%s %s -%c -R %s -s %d" % \
                (
                    INJECTOR,
                    " ".join(self.settings.args),
                    self.settings.synth_mode,
                    "-0" if self.settings.root else "",
                    self.settings.seed
                )
        self.process = subprocess.Popen(
            "exec %s" % self.command,
            shell=True,
            stdout=subprocess.PIPE,
            stdin=subprocess.PIPE,
            preexec_fn=os.setsid
            ) 
Example #28
Source File: calcs.py    From mlearn with BSD 3-Clause "New" or "Revised" License 6 votes vote down vote up
def calculate(self):
        """
        Calculate the NEB barrier given Potential class.
        """
        with ScratchDir('.'):
            input_file = self._setup()
            p = subprocess.Popen(['mpirun', '-n', str(self.num_replicas),
                                  'lmp_mpi', '-partition', '{}x1'.format(self.num_replicas),
                                  '-in', input_file],
                                 stdout=subprocess.PIPE)
            stdout = p.communicate()[0]
            rc = p.returncode
            if rc != 0:
                error_msg = 'LAMMPS exited with return code %d' % rc
                msg = stdout.decode("utf-8").split('\n')[:-1]
                try:
                    error_line = [i for i, m in enumerate(msg)
                                  if m.startswith('ERROR')][0]
                    error_msg += ', '.join([e for e in msg[error_line:]])
                except Exception:
                    error_msg += msg[-1]
                raise RuntimeError(error_msg)
            result = self._parse()
        return result 
Example #29
Source File: calcs.py    From mlearn with BSD 3-Clause "New" or "Revised" License 5 votes vote down vote up
def calculate(self, structures):
        """
        Perform the calculation on a series of structures.

        Args:
            structures [Structure]: Input structures in a list.

        Returns:
            List of computed data corresponding to each structure,
            varies with different subclasses.

        """
        for s in structures:
            assert self._sanity_check(s) is True, \
                'Incompatible structure found'
        ff_elements = None
        if hasattr(self, 'element_profile'):
            ff_elements = self.element_profile.keys()
        with ScratchDir('.'):
            input_file = self._setup()
            data = []
            for s in structures:
                ld = LammpsData.from_structure(s, ff_elements)
                ld.write_file('data.static')
                p = subprocess.Popen([self.LMP_EXE, '-in', input_file],
                                     stdout=subprocess.PIPE)
                stdout = p.communicate()[0]
                rc = p.returncode
                if rc != 0:
                    error_msg = 'LAMMPS exited with return code %d' % rc
                    msg = stdout.decode("utf-8").split('\n')[:-1]
                    try:
                        error_line = [i for i, m in enumerate(msg)
                                      if m.startswith('ERROR')][0]
                        error_msg += ', '.join([e for e in msg[error_line:]])
                    except Exception:
                        error_msg += msg[-1]
                    raise RuntimeError(error_msg)
                results = self._parse()
                data.append(results)
        return data 
Example #30
Source File: versioneer.py    From NiBetaSeries with MIT License 5 votes vote down vote up
def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
                env=None):
    """Call the given command(s)."""
    assert isinstance(commands, list)
    p = None
    for c in commands:
        try:
            dispcmd = str([c] + args)
            # remember shell=False, so use git.cmd on windows, not just git
            p = subprocess.Popen([c] + args, cwd=cwd, env=env,
                                 stdout=subprocess.PIPE,
                                 stderr=(subprocess.PIPE if hide_stderr
                                         else None))
            break
        except EnvironmentError:
            e = sys.exc_info()[1]
            if e.errno == errno.ENOENT:
                continue
            if verbose:
                print("unable to run %s" % dispcmd)
                print(e)
            return None, None
    else:
        if verbose:
            print("unable to find command, tried %s" % (commands,))
        return None, None
    stdout = p.communicate()[0].strip()
    if sys.version_info[0] >= 3:
        stdout = stdout.decode()
    if p.returncode != 0:
        if verbose:
            print("unable to run %s (error)" % dispcmd)
            print("stdout was %s" % stdout)
        return None, p.returncode
    return stdout, p.returncode