dpdispatcher 0.6.11__py3-none-any.whl → 0.6.12__py3-none-any.whl

dpdispatcher/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.6.11'
-__version_tuple__ = version_tuple = (0, 6, 11)
+__version__ = version = '0.6.12'
+__version_tuple__ = version_tuple = (0, 6, 12)
 
 __commit_id__ = commit_id = None

dpdispatcher/contexts/dp_cloud_server_context.py

@@ -161,7 +161,9 @@ class BohriumContext(BaseContext):
         # return oss_task_zip
         # api.upload(self.oss_task_dir, zip_task_file)
 
-    def download(self, submission):
+    def download(
+        self, submission, check_exists=False, mark_failure=True, back_error=False
+    ):
         jobs = submission.belonging_jobs
         job_hashs = {}
         job_infos = {}

dpdispatcher/contexts/lazy_local_context.py

@@ -83,7 +83,7 @@ class LazyLocalContext(BaseContext):
 
     def upload(
         self,
-        jobs,
+        submission,
         # local_up_files,
         dereference=True,
     ):
@@ -91,7 +91,7 @@ class LazyLocalContext(BaseContext):
 
     def download(
         self,
-        jobs,
+        submission,
         # remote_down_files,
         check_exists=False,
         mark_failure=True,

dpdispatcher/contexts/openapi_context.py

@@ -95,11 +95,11 @@ class OpenAPIContext(BaseContext):
             raise ValueError(
                 "remote_profile must contain 'project_id' or set environment variable 'BOHRIUM_PROJECT_ID'"
             )
-        self.client = Bohrium(
+        self.client = Bohrium(  # type: ignore[reportPossiblyUnboundVariable]
             access_key=access_key, project_id=project_id, app_key=app_key
         )
-        self.storage = Tiefblue()
-        self.job = Job(client=self.client)
+        self.storage = Tiefblue()  # type: ignore[reportPossiblyUnboundVariable]
+        self.job = Job(client=self.client)  # type: ignore[reportPossiblyUnboundVariable]
         self.jgid = None
         os.makedirs(DP_CLOUD_SERVER_HOME_DIR, exist_ok=True)
 
@@ -206,7 +206,9 @@ class OpenAPIContext(BaseContext):
         # return oss_task_zip
         # api.upload(self.oss_task_dir, zip_task_file)
 
-    def download(self, submission):
+    def download(
+        self, submission, check_exists=False, mark_failure=True, back_error=False
+    ):
         jobs = submission.belonging_jobs
         job_hashs = {}
         job_infos = {}

dpdispatcher/contexts/ssh_context.py

@@ -45,6 +45,7 @@ class SSHSession:
         tar_compress=True,
         look_for_keys=True,
         execute_command=None,
+        proxy_command=None,
     ):
         self.hostname = hostname
         self.username = username
@@ -58,6 +59,7 @@ class SSHSession:
         self.tar_compress = tar_compress
         self.look_for_keys = look_for_keys
         self.execute_command = execute_command
+        self.proxy_command = proxy_command
         self._keyboard_interactive_auth = False
         self._setup_ssh()
 
@@ -142,7 +144,12 @@ class SSHSession:
         # transport = self.ssh.get_transport()
         sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
         sock.settimeout(self.timeout)
-        sock.connect((self.hostname, self.port))
+
+        # Use ProxyCommand if configured (either directly or via jump host parameters)
+        if self.proxy_command is not None:
+            sock = paramiko.ProxyCommand(self.proxy_command)
+        else:
+            sock.connect((self.hostname, self.port))
 
         # Make a Paramiko Transport object using the socket
         ts = paramiko.Transport(sock)
@@ -340,6 +347,9 @@ class SSHSession:
             "enable searching for discoverable private key files in ~/.ssh/"
         )
         doc_execute_command = "execute command after ssh connection is established."
+        doc_proxy_command = (
+            "ProxyCommand to use for SSH connection through intermediate servers."
+        )
         ssh_remote_profile_args = [
             Argument("hostname", str, optional=False, doc=doc_hostname),
             Argument("username", str, optional=False, doc=doc_username),
@@ -388,6 +398,13 @@ class SSHSession:
                 default=None,
                 doc=doc_execute_command,
             ),
+            Argument(
+                "proxy_command",
+                [str, type(None)],
+                optional=True,
+                default=None,
+                doc=doc_proxy_command,
+            ),
         ]
         ssh_remote_profile_format = Argument(
             "ssh_session", dict, ssh_remote_profile_args
@@ -396,23 +413,37 @@ class SSHSession:
 
     def put(self, from_f, to_f):
         if self.rsync_available:
+            # For rsync, we need to use %h:%p placeholders for target host/port
+            proxy_cmd_rsync = None
+            if self.proxy_command is not None:
+                proxy_cmd_rsync = self.proxy_command.replace(
+                    f"{self.hostname}:{self.port}", "%h:%p"
+                )
             return rsync(
                 from_f,
                 self.remote + ":" + to_f,
                 port=self.port,
                 key_filename=self.key_filename,
                 timeout=self.timeout,
+                proxy_command=proxy_cmd_rsync,
             )
         return self.sftp.put(from_f, to_f)
 
     def get(self, from_f, to_f):
         if self.rsync_available:
+            # For rsync, we need to use %h:%p placeholders for target host/port
+            proxy_cmd_rsync = None
+            if self.proxy_command is not None:
+                proxy_cmd_rsync = self.proxy_command.replace(
+                    f"{self.hostname}:{self.port}", "%h:%p"
+                )
             return rsync(
                 self.remote + ":" + from_f,
                 to_f,
                 port=self.port,
                 key_filename=self.key_filename,
                 timeout=self.timeout,
+                proxy_command=proxy_cmd_rsync,
             )
         return self.sftp.get(from_f, to_f)
 
@@ -825,8 +856,8 @@ class SSHContext(BaseContext):
         # print(pid)
         return {"stdin": stdin, "stdout": stdout, "stderr": stderr}
 
-    def check_finish(self, cmd_pipes):
-        return cmd_pipes["stdout"].channel.exit_status_ready()
+    def check_finish(self, proc):
+        return proc["stdout"].channel.exit_status_ready()
 
     def get_return(self, cmd_pipes):
         if not self.check_finish(cmd_pipes):
@@ -888,11 +919,11 @@ class SSHContext(BaseContext):
         # local tar
         if os.path.isfile(os.path.join(self.local_root, of)):
             os.remove(os.path.join(self.local_root, of))
-        with tarfile.open(
+        with tarfile.open(  # type: ignore[reportCallIssue, reportArgumentType]
             os.path.join(self.local_root, of),
-            tarfile_mode,
-            dereference=dereference,
-            **kwargs,
+            mode=tarfile_mode,  # type: ignore[reportArgumentType]
+            dereference=dereference,  # type: ignore[reportArgumentType]
+            **kwargs,  # type: ignore[reportArgumentType]
         ) as tar:
             # avoid compressing duplicated files or directories
             for ii in set(files):

dpdispatcher/machine.py

@@ -227,7 +227,7 @@ class Machine(metaclass=ABCMeta):
         return if_recover
 
     @abstractmethod
-    def check_finish_tag(self, **kwargs):
+    def check_finish_tag(self, job):
         raise NotImplementedError(
             "abstract method check_finish_tag should be implemented by derived class"
         )

dpdispatcher/machines/JH_UniScheduler.py

@@ -84,9 +84,6 @@ class JH_UniScheduler(Machine):
         self.context.write_file(job_id_name, job_id)
         return job_id
 
-    def default_resources(self, resources):
-        pass
-
     @retry()
     def check_status(self, job):
         try:

dpdispatcher/machines/fugaku.py

@@ -67,9 +67,6 @@ class Fugaku(Machine):
         self.context.write_file(job_id_name, job_id)
         return job_id
 
-    def default_resources(self, resources):
-        pass
-
     def check_status(self, job):
         job_id = job.job_id
         if job_id == "":

dpdispatcher/machines/lsf.py

@@ -102,9 +102,6 @@ class LSF(Machine):
         return job_id
 
     # TODO: derive abstract methods
-    def default_resources(self, resources):
-        pass
-
     def sub_script_cmd(self, res):
         pass
 

dpdispatcher/machines/openapi.py

@@ -64,11 +64,11 @@ class OpenAPI(Machine):
             raise ValueError(
                 "remote_profile must contain 'project_id' or set environment variable 'BOHRIUM_PROJECT_ID'"
             )
-        self.client = Bohrium(
+        self.client = Bohrium(  # type: ignore[reportPossiblyUnboundVariable]
             access_key=access_key, project_id=project_id, app_key=app_key
         )
-        self.storage = Tiefblue()
-        self.job = Job(client=self.client)
+        self.storage = Tiefblue()  # type: ignore[reportPossiblyUnboundVariable]
+        self.job = Job(client=self.client)  # type: ignore[reportPossiblyUnboundVariable]
         self.group_id = None
 
     def gen_script(self, job):

dpdispatcher/machines/pbs.py

@@ -69,9 +69,6 @@ class PBS(Machine):
         self.context.write_file(job_id_name, job_id)
         return job_id
 
-    def default_resources(self, resources):
-        pass
-
     def check_status(self, job):
         job_id = job.job_id
         if job_id == "":
@@ -255,9 +252,6 @@ class SGE(PBS):
         self.context.write_file(job_id_name, job_id)
         return job_id
 
-    def default_resources(self, resources):
-        pass
-
     def check_status(self, job):
         ### https://softpanorama.org/HPC/Grid_engine/Queues/queue_states.shtml
         job_id = job.job_id

dpdispatcher/machines/shell.py

@@ -60,9 +60,6 @@ class Shell(Machine):
         # self.context.write_file(job_id_name, job_id)
         # return job_id
 
-    def default_resources(self, resources):
-        pass
-
     def check_status(self, job):
         job_id = job.job_id
         # print('shell.check_status.job_id', job_id)

dpdispatcher/machines/slurm.py

@@ -118,9 +118,6 @@ class Slurm(Machine):
         self.context.write_file(job_id_name, job_id)
         return job_id
 
-    def default_resources(self, resources):
-        pass
-
     @retry()
     def check_status(self, job):
         job_id = job.job_id

dpdispatcher/utils/dpcloudserver/client.py

@@ -142,10 +142,10 @@ class Client:
         res = self.get("/data/get_sts_token", {})
         # print('debug>>>>>>>>>>>>>', res)
         dlog.debug(f"debug: _get_oss_bucket: res:{res}")
-        auth = oss2.StsAuth(
+        auth = oss2.StsAuth(  # type: ignore[reportPossiblyUnboundVariable]
             res["AccessKeyId"], res["AccessKeySecret"], res["SecurityToken"]
         )
-        return oss2.Bucket(auth, endpoint, bucket_name)
+        return oss2.Bucket(auth, endpoint, bucket_name)  # type: ignore[reportPossiblyUnboundVariable]
 
     def download(self, oss_file, save_file, endpoint, bucket_name):
         bucket = self._get_oss_bucket(endpoint, bucket_name)
@@ -184,7 +184,7 @@ class Client:
         )
         bucket = self._get_oss_bucket(endpoint, bucket_name)
         total_size = os.path.getsize(zip_task_file)
-        part_size = determine_part_size(total_size, preferred_size=1000 * 1024)
+        part_size = determine_part_size(total_size, preferred_size=1000 * 1024)  # type: ignore[reportPossiblyUnboundVariable]
         upload_id = bucket.init_multipart_upload(oss_task_zip).upload_id
         parts = []
         with open(zip_task_file, "rb") as fileobj:
@@ -196,9 +196,9 @@ class Client:
                     oss_task_zip,
                     upload_id,
                     part_number,
-                    SizedFileAdapter(fileobj, num_to_upload),
+                    SizedFileAdapter(fileobj, num_to_upload),  # type: ignore[reportPossiblyUnboundVariable]
                 )
-                parts.append(PartInfo(part_number, result.etag))
+                parts.append(PartInfo(part_number, result.etag))  # type: ignore[reportPossiblyUnboundVariable]
                 offset += num_to_upload
                 part_number += 1
         # result = bucket.complete_multipart_upload(oss_task_zip, upload_id, parts)

dpdispatcher/utils/utils.py

@@ -2,6 +2,7 @@ import base64
 import hashlib
 import hmac
 import os
+import shlex
 import struct
 import subprocess
 import time
@@ -89,6 +90,7 @@ def rsync(
     port: int = 22,
     key_filename: Optional[str] = None,
     timeout: Union[int, float] = 10,
+    proxy_command: Optional[str] = None,
 ):
     """Call rsync to transfer files.
 
@@ -104,6 +106,8 @@ def rsync(
         identity file name
     timeout : int, default=10
         timeout for ssh
+    proxy_command : str, optional
+        ProxyCommand to use for SSH connection
 
     Raises
     ------
@@ -124,20 +128,30 @@ def rsync(
     ]
     if key_filename is not None:
         ssh_cmd.extend(["-i", key_filename])
+
+    # Use proxy_command if provided
+    if proxy_command is not None:
+        ssh_cmd.extend(["-o", f"ProxyCommand={proxy_command}"])
+
+    # Properly escape the SSH command for rsync's -e option
+    ssh_cmd_str = " ".join(shlex.quote(part) for part in ssh_cmd)
+
     cmd = [
         "rsync",
-        # -a: archieve
-        # -z: compress
-        "-az",
+        # -r: recursive, -l: links, -p: perms, -t: times, -D: devices/specials
+        # -z: compress (exclude -o: owner, -g: group to avoid permission issues)
+        "-rlptDz",
         "-e",
-        " ".join(ssh_cmd),
+        ssh_cmd_str,
         "-q",
         from_file,
         to_file,
     ]
-    ret, out, err = run_cmd_with_all_output(cmd, shell=False)
+    # Convert to string for shell=True
+    cmd_str = " ".join(shlex.quote(arg) for arg in cmd)
+    ret, out, err = run_cmd_with_all_output(cmd_str, shell=True)
     if ret != 0:
-        raise RuntimeError(f"Failed to run {cmd}: {err}")
+        raise RuntimeError(f"Failed to run {cmd_str}: {err}")
 
 
 class RetrySignal(Exception):

{dpdispatcher-0.6.11.dist-info → dpdispatcher-0.6.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dpdispatcher
-Version: 0.6.11
+Version: 0.6.12
 Summary: Generate HPC scheduler systems jobs input scripts, submit these scripts to HPC systems, and poke until they finish
 Author: DeepModeling
 License:                    GNU LESSER GENERAL PUBLIC LICENSE

{dpdispatcher-0.6.11.dist-info → dpdispatcher-0.6.12.dist-info}/RECORD

@@ -1,49 +1,49 @@
 dpdispatcher/__init__.py,sha256=CLZP_N5CTp14ujWCykEHuJjoIfKR6CwrclXhjWUgNoE,517
 dpdispatcher/__main__.py,sha256=BFhG-mSBzVZUEezQJqXWZnt2WsnhAHT_zpT8Y6gpOz0,116
-dpdispatcher/_version.py,sha256=sw6_B_LEWeMBiN2AFkGTSamIubZxwWvM45JyuClFrPY,706
+dpdispatcher/_version.py,sha256=a-0leJ4HihsyvhxqpbGKODhfNk5qw_xjChcx488fqoI,706
 dpdispatcher/arginfo.py,sha256=pNaxYIE6ahBidpR7OCKZdw8iGt003uTXGSlVzwiuvRg,188
 dpdispatcher/base_context.py,sha256=W4eWDWVzYeL6EuEkivmJp-_h_B2mV9PtRWc09l1_Qzc,5242
 dpdispatcher/dlog.py,sha256=QJKAwB6gV3Zb6zQUL9dZ_uIoTIEy9Z7ecmVQ-8WNmD8,1081
 dpdispatcher/dpdisp.py,sha256=jhuTmwPY7KBF4WukaQomEwZcfYoISaMbKwuxdDGSluc,4206
-dpdispatcher/machine.py,sha256=k53ycs_v7xrl4D93URc5ht0shoO9NPrVl0rYr4v5OiU,16696
+dpdispatcher/machine.py,sha256=bW4oEpmDKwMHrMESFMgQbUxG3N1xUh3Z4NRY1uxz73I,16691
 dpdispatcher/run.py,sha256=tFHbJAioXXpgHTE5bhRRAuc8w7cX1ET9SBbiAg3Rw-I,5382
 dpdispatcher/submission.py,sha256=zLzdKJkMXhvaicD2el33NxDHP_9LL29HBombxR1l-Sw,48086
 dpdispatcher/contexts/__init__.py,sha256=jlvcIppmUnS39yBlkZEDvIQFV-j_BR75ZTbZALF_RB0,336
-dpdispatcher/contexts/dp_cloud_server_context.py,sha256=PGRMef3q2hfK-o5dNIWWvzPca2NK1HrWEgungM4L9Go,12420
+dpdispatcher/contexts/dp_cloud_server_context.py,sha256=pdzQuG-j8sdNsindqwStWwu6OA0fZauCtj7FyWh_014,12491
 dpdispatcher/contexts/hdfs_context.py,sha256=mYQzXMZ4A9EjjWBAH3Ba6HOErUhMMwCsKxOjpd5R57Y,9105
-dpdispatcher/contexts/lazy_local_context.py,sha256=FAClbLD2F4LizUqFzMOg3t0Z6NLeTDLJy7NkRcDELFs,5070
+dpdispatcher/contexts/lazy_local_context.py,sha256=IyDBIKGRz0Ctur4VX1zA78kMi2lf6ZNRcZm_RnFkZSk,5082
 dpdispatcher/contexts/local_context.py,sha256=VbaSXGAc_EDMT0K5WV_flBF0bX87ntrwO_hq_Bkcb04,14590
-dpdispatcher/contexts/openapi_context.py,sha256=bWfg-y-QHAT1iSva6PvuLgMs1uJDLom4QC06IGMeUfs,11928
-dpdispatcher/contexts/ssh_context.py,sha256=VOpPRQX1WS6WbWxCYhuT62q203v1Qx_hygLsV41p3Fg,37585
+dpdispatcher/contexts/openapi_context.py,sha256=0DKlgux-1zmUuS28AK1hy_n16n6uCTugI9xjjnKefnI,12140
+dpdispatcher/contexts/ssh_context.py,sha256=0Ah3fdgq0uZxWh4kLS6UbVmaQFgCZ2bsZTwTXVa_k-M,39048
 dpdispatcher/dpcloudserver/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dpdispatcher/dpcloudserver/client.py,sha256=k1niKjG6zFnMtHn_UuCjYoOcMju3o3PV-GdyVLr5-KM,165
 dpdispatcher/entrypoints/__init__.py,sha256=exKSFT3j2oCerGwtI8WbHQK-D0K-CyifocRji1xntT4,20
 dpdispatcher/entrypoints/gui.py,sha256=29lMXqbmSRbLj4rfBv7Jnw89NLU9syTB88IUP6IRJsU,830
 dpdispatcher/entrypoints/run.py,sha256=tRkHfeAktV6gF31yb2MVOSTlpNGZFw3N0jHBmM1YfIg,175
 dpdispatcher/entrypoints/submission.py,sha256=ikVwIZAQL0SsYO5xaMIdKXgO6qtc05w1vqmvtG7Nk5M,3401
-dpdispatcher/machines/JH_UniScheduler.py,sha256=ZeUZXqyGrN5Zec4gwpwH5r6FJXaJLRUJMQWDCP7X3Nk,5756
+dpdispatcher/machines/JH_UniScheduler.py,sha256=6A4lnZUIbsR501STkXyKEJCVaq-iJguzlfVuHq9ZRf4,5698
 dpdispatcher/machines/__init__.py,sha256=tOQuPUlW1Ab4qcC0oSAIyDjZA_WyE67h_EIxPCWGhys,336
 dpdispatcher/machines/distributed_shell.py,sha256=c0-lGeGz_M-PY2gPciT-uYZLQht5XTMaxJSNxkbMffc,7489
 dpdispatcher/machines/dp_cloud_server.py,sha256=SR69gsFb2BvOQCW1QnWfP3cQvu_qHLJNsycp5wzosJU,11706
-dpdispatcher/machines/fugaku.py,sha256=oY2hD2ldL2dztwtJ9WNisdsfPnaX-5yTRXewIT9r60I,4314
-dpdispatcher/machines/lsf.py,sha256=xGDq8OLAk83E9EjK_3-QtEOyahvBGspWbxT__7mnSTw,7896
-dpdispatcher/machines/openapi.py,sha256=8unjG9HTCBwbkZTW_t-QKOSaBHfqhzsMARTVVCDGGHw,9929
-dpdispatcher/machines/pbs.py,sha256=gUoj3OGQbZRBK4P-WXlhrxlQqTeUi9X8JGLOkAB__wE,12669
-dpdispatcher/machines/shell.py,sha256=EeYnRCowXdzO3Nh25Yh_t5xeM6frq4uChk4GVx7OjH8,4797
-dpdispatcher/machines/slurm.py,sha256=rN51Qh_u9ZVmjkIClu4Tfc-Qesr19DxPaaeh0FmRx14,15413
+dpdispatcher/machines/fugaku.py,sha256=BlaUfgHoGABROuZeT5byr12rXCVCqahXISL57SUObX0,4256
+dpdispatcher/machines/lsf.py,sha256=BH-lvXGkoCOAYJWAX7boE1TQtPfyMsRjmShIdnZ-MBE,7838
+dpdispatcher/machines/openapi.py,sha256=TXwXGYRB35049MU76-6SBinxSqvh11ey3iWYj8bqEi8,10070
+dpdispatcher/machines/pbs.py,sha256=9QsOKxyGc4fPRxBmFhQ1rlNzRlpmbSe6WvvkZj_0Q0o,12553
+dpdispatcher/machines/shell.py,sha256=hZwrIsT-GzXToCobrrmxY0GBoNy0BEH4oTK5MpQE1H4,4739
+dpdispatcher/machines/slurm.py,sha256=Rf8aV_HxpSLiQ5WC-8nUoGXjAaPsttrGu9ZV6ijYsXg,15355
 dpdispatcher/utils/__init__.py,sha256=fwvwkMf7DFNQkNBiIce8Y8gRA6FhICwKjkKiXu_BEJg,13
 dpdispatcher/utils/hdfs_cli.py,sha256=a1a9PJAzt3wsTcdaSw_oD1vcNw59pMooxpAHjYOaaGA,5209
 dpdispatcher/utils/job_status.py,sha256=Eszs4TPLfszCuf6zLaFonf25feXDUguF28spYOjJpQE,233
 dpdispatcher/utils/record.py,sha256=c8jdPmCuLzRmFo_jOjR0j9zFR1EWX3NSHVuPEIYCycg,2147
-dpdispatcher/utils/utils.py,sha256=Wo-8tGO05e2KkRyLXoIg3UlxzkuM-x1phRrTA1Hh7Ko,5328
+dpdispatcher/utils/utils.py,sha256=CSDzc3VhoF8HvEMaBiH-CSk6WnKFeORXzYcKHhBA4Dg,5940
 dpdispatcher/utils/dpcloudserver/__init__.py,sha256=FnX9HH-2dXADluNfucg98JPMfruMoBpN9ER9lZkVQvQ,49
-dpdispatcher/utils/dpcloudserver/client.py,sha256=fp1e14MTgsMgasZSWowq-NqfCoi21PnCrH1igCQVxFU,12179
+dpdispatcher/utils/dpcloudserver/client.py,sha256=BKKZyY5VblkIace2muFsvSX_7uEgM8E_IZBXaPtaT4I,12414
 dpdispatcher/utils/dpcloudserver/config.py,sha256=NteQzf1OeEkz2UbkXHHQ0B72cUu23zLVzpM9Yh4v1Cc,559
 dpdispatcher/utils/dpcloudserver/retcode.py,sha256=1qAF8gFZx55u2sO8KbtYSIIrjcO-IGufEUlwbkSfC1g,721
 dpdispatcher/utils/dpcloudserver/zip_file.py,sha256=f9WrlktwHW0YipaWg5Y0kxjMZlhD1cJYa6EUpvu4Cro,2611
-dpdispatcher-0.6.11.dist-info/licenses/LICENSE,sha256=46mU2C5kSwOnkqkw9XQAJlhBL2JAf1_uCD8lVcXyMRg,7652
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