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Information -====================== - -This component offers the main information about your experiment. - -.. figure:: fig_experiment.jpg - :name: experiment_view - :width: 100% - :align: center - :alt: experiment_view - - Experiment Information - -At the top left you see the ``Autosubmit Searcher`` home link that will take you back to the :ref:`autosubmitGUIMP`, next to it you see the ``Home`` link that serves the same purpose, then you see the ``About`` link that takes you to a page with important information about the application (including the link to this documentation). Then you see the experiment name and ``status``, which is updated every 5 minutes. - -At the bottom you see some relevant metadata, including the ``branch`` of the ``model`` that was used in the experiment, the ``HPC name`` targeted by the experiment, the owned, and the last time the experiment folder was modified, which probably coincides with the creation date of the experiment. - -On the center you see the :ref:`treeRepresentation`, which is loaded automatically when you open this page. \ No newline at end of file diff --git a/docs/build/html/_sources/agui/graph.rst.txt b/docs/build/html/_sources/agui/graph.rst.txt deleted file mode 100644 index f8c3af5a74f9b425423f2aa7c55183a3be6aad42..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/agui/graph.rst.txt +++ /dev/null @@ -1,93 +0,0 @@ -.. _graphRepresentation: - -Graph Representation -==================== - -The Graph Representation of the experiment offers a dependency oriented view. - -.. figure:: fig_graph_2.jpg - :name: experiment_graph - :width: 100% - :align: center - :alt: Experiment Graph 1 - - Experiment Graph Representation - -This view offers a graph representation of the experiments where a node represents a job and an edge represents a directed dependency relationship between nodes. To open it you must click on the button ``Classic``, which is the basic representation that uses either ``GraphViz`` or an heuristic approach depending on experiment complexity; we explain the other options later. - -Once the graph representation is loaded, it will focus on a relevant node according to some established rules. The color of each node represents the status of the job it represents: you can see a color guide at the bottom of the page in the form of buttons. If you click in any of those buttons, the graph will focus on the last node with that status, except in the case of ``WAITING`` where the graph will focus on the first one. You can navigate the graph in this way, but there are other navigation buttons at the left and right corners of the graph canvas. You can also use your mouse or trackpad to navigate the graph, zoom in or zoom out. Below each node you can see the ``job name`` of the job it represents. - -.. important:: For some experiments you will get a well distributed and generally good looking graph representation, for others you get a more straightforward representation. It depends on the size and dependency complexity of your experiments, not all experiments can be modeled as a good looking graph in reasonable time. - -When you click on a node, you can see on the right panel (**Selection Panel**) the following information: - -- *Initial*: Initial date as in the one used for grouping. -- *Real*: Real date after adding to the initial date the number of chunk units depending on chunk size. -- *Section*: Also known as job type. -- *Member* -- *Chunk* -- *Platform*: HPC Platform. -- *Processors*: Number of processors required by the job. -- *Wallclock*: Time requested by the job. -- *Queue*: Time spent in queue, in minutes. -- *Run*: Time spent running, in minutes. -- *Status*: Job status. -- *Out*: Button that opens a list of jobs that depend on the one selected. -- *In*: Button that opens a list of jobs on which the selected job depends. -- *out path*: Path to the .out log file. -- *err path*: Path to the .err log file. - -Wrappers Representation ------------------------ - -Wrappers are an important feature of Autosubmit, and as such, it should be possible to visualize them in the graph representation. - -.. figure:: fig_graph_3.jpg - :name: experiment_graph_wr - :width: 100% - :align: center - :alt: Experiment Graph Wrapper - - Wrapper Graph Representation - - -Wrappers are represented by nodes that have dashed border, hexagon or square shape (no difference between them), and that share green background edges. On the right side of the graph you can find the **Wrappers Tab** and it will display a list of the existing wrappers as buttons. If you click on any of these buttons, the nodes that belong to that wrapper will be highlighted. - -Monitoring ----------- - -If the experiment is ``RUNNING`` you will see at the top right corner the button ``Start Job Monitor``. When you click on it, a live **Job Monitor** will be initialized and the status of the jobs and wrappers will be queried every minute, any change will be updated in the graph. Also, if the **Job Monitor** is running, the detected changes will be listed in a panel **Monitor Panel** below the **Selection Panel**. You can stop this process by clicking on the button **Stop Job Monitor**. - -.. important:: While this is a good option to monitor the progress of your experiment, you can also use the :ref:`log`. - -Job Search ----------- - -.. figure:: fig_graph_4.jpg - :name: experiment_graph_search - :width: 100% - :align: center - :alt: Job Search - - Job Search in Graph - -On top of the graph you will see an input text box following by the button ``Seach by Job Name``. Insert into that box the string that you want to find and the engine will build an internal list of those jobs whose name coincides with that string. For example ``_LOCAL_`` will show only jobs whose title contain the that string. Buttons ``Previous`` and ``Next`` will appear and next to them the number of jobs that coincide with your search, you can use these buttons to traverse the graph highlighting the nodes included in the resulting internal list. - -Grouped by Date Member ----------------------- - -By clicking on the button ``Grouped by D-M`` you get a graph representation where the nodes are clustered by date and member. For example, if your experiment has only one starting date and one member, then you will have only one cluster in this view. These clusters are represented by rectangular boxes whose color gives a general idea of the status of the jobs inside it. - -.. important:: You can double click on any cluster to "open" it, meaning that the nodes that belong to that cluster will be freed and positioned individually. - -Grouped by Status ------------------ - -By clicking on the button ``Grouped by Status`` you get a graph representation where the nodes are clustered by status into 3 clusters: ``WAITING``, ``COMPLETED``, and ``SUSPENDED``. Same rules mentioned for **Grouped by Date Member** apply. - -Laplacian ---------- - -By clicking on the button ``Laplacian`` you get a graph representation where the ``(x,y)`` coordinates of each node are calculated based on the second and third smallest eigenvector of the Graph Laplacian. All functionality is supported. - - diff --git a/docs/build/html/_sources/agui/log.rst.txt b/docs/build/html/_sources/agui/log.rst.txt deleted file mode 100644 index 1cd40275bb41472fa88e38dea21f571256654488..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/agui/log.rst.txt +++ /dev/null @@ -1,34 +0,0 @@ -.. _log: - -Autosubmit Log -============== - -When you click on the ``Log`` tab, you will see the button ``Show Log``: - -.. figure:: fig_log_1.jpg - :name: experiment_log - :width: 100% - :align: center - :alt: Experiment Log 1 - - Experiment Log - -.. important:: The main Autosubmit log is usually stored in the folder ``/tmp/`` of your experiment, and this is the first path the system will scan. - -When you click on the ``Show Log`` button, the last 150 lines of the log will be displayed: - -.. figure:: fig_log_2.jpg - :name: experiment_log_open - :width: 100% - :align: center - :alt: Experiment Log 2 - - Experiment Log Open - - -At the top of the log you will see the name of the log file that is being displayed along with the timestamp of the last time the log was requested, and to the right you see this timestamp in ``datetime`` format. - -If the experiment is currently running, the log will be updated periodically to keep you up with recent updates in the experiment execution. It is possible to scroll this view. - -If you click on ``Hide Log`` the log will be cleared and the periodic updates will stop. - diff --git a/docs/build/html/_sources/agui/statistics.rst.txt b/docs/build/html/_sources/agui/statistics.rst.txt deleted file mode 100644 index 1756dabbb68cac8a36a889149b472e7ca1fb7447..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/agui/statistics.rst.txt +++ /dev/null @@ -1,31 +0,0 @@ -.. _statistics: - -Autosubmit Statistics -===================== - - -When you click on the ``Statistics`` tab, you will see two input boxes: ``Section`` and ``Hours``, followed by the button ``Get Statistics``: - -.. figure:: fig_stat_1.jpg - :name: experiment_stats - :width: 100% - :align: center - :alt: Experiment Stat 1 - - Experiment Statistics - -There is also a brief explanation of the input fields and expected result. Basically, ``Section`` allows you to narrow your search to certain job types, and ``Hours`` allows you to set a time limit to look into the past in hours. - -In this example we have queried 3 hours into the past: - -.. figure:: fig_stat_2.jpg - :name: experiment_stats_open - :width: 100% - :align: center - :alt: Experiment Stat 2 - - Experiment Statistics (Last 3 hours) - -Click on the button ``Clear Statistics`` to clear the results and submit another query. - -.. important:: For more details about Autosubmit statistics, refer to: :ref:`autoStatistics`. \ No newline at end of file diff --git a/docs/build/html/_sources/agui/tree.rst.txt b/docs/build/html/_sources/agui/tree.rst.txt deleted file mode 100644 index 88e4eac4ba9c8d1427ecba75ce4de4552ef3bf9e..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/agui/tree.rst.txt +++ /dev/null @@ -1,68 +0,0 @@ -.. _treeRepresentation: - -Tree Representation -=================== - -The Tree Representation offers a structured view of the experiment. - -.. figure:: fig_tree_2.jpg - :name: experiment_tree - :width: 100% - :align: center - :alt: Experiment Tree 1 - - Experiment Tree Representation - -The view is organized in groups by ``date``, and ``date-member``. Each group has a folder icon, and next to the icon you can find the progress of the group as ``completed / total`` jobs (when all the jobs in a group have been completed, a check symbol will appear); then, an indicator of how many jobs inside that group are **RUNNING**, **QUEUING**, or have **FAILED**. Furthermore, if wrappers exist in the experiment, independent groups will be added for each wrapper that will contain the list of jobs included in the corresponding wrapper. This implies that a job can be repeated: once inside its ``date-member`` group and once in its wrapper group. - -Inside each group you will find the list of jobs that belong to that group. The jobs are shown following this format: *job name* + # *job status* + ( + *queuing time* + ) + *running time*. Jobs that belong to a wrapper have also a badge with the code of the wrapper. - -When you click on a Job, you can see on the right panel (**Selection Panel**) the following information: - -- *Initial*: Initial date as in the one used for grouping. -- *Real*: Real date after adding to the initial date the number of chunk units depending on chunk size. -- *Section*: Also known as job type. -- *Member* -- *Chunk* -- *Platform*: HPC Platform. -- *Processors*: Number of processors required by the job. -- *Wallclock*: Time requested by the job. -- *Queue*: Time spent in queue, in minutes. -- *Run*: Time spent running, in minutes. -- *Status*: Job status. -- *Out*: Button that opens a list of jobs that depend on the one selected. -- *In*: Button that opens a list of jobs on which the selected job depends. -- *Wrapper*: If the job belongs to a wrapper, the name of the wrapper will be shown. -- *Code*: Code of the wrapper the job belongs to, for easy searching. -- *out path*: Path to the .out log file. -- *err path*: Path to the .err log file. - -Monitoring ----------- - -If the experiment status is **RUNNING**, you will see a button called **Refresh** at the top right corner. This button will update the information of the jobs in the tree if necessary. Next to this button, you will see the button **Start Job Monitor**. When you click on it, a live **Job Monitor** will be initialized and the status of the jobs and wrappers will be queried every minute, any change will be updated in the **Tree View**. Also, if the **Job Monitor** is running, the detected changes will be listed in a panel **Monitor Panel** below the **Selection Panel**. You can stop this process by clicking on the button **Stop Job Monitor**. - -The button **Clear Tree View** will clear the Tree Representation. It is also a valid way to refresh the Tree View. - -Filter ------- - -At the top left you can find the **Filter text** input box. Insert any string and the list will show only those jobs whose description coincides with that string. For example ``#COMPLETED`` will show only completed jobs, ``Wrapped`` will show only those jobs that belong to a wrapper, ``_fc0_`` will show only those jobs that belong to the fc0 member. Press **Clear** to reset the filter. On the right side of this bar, you will see the total number of jobs, and the chunk unit used in the experiment. - -Advanced Filter ---------------- - -It is possible to use the keychar ``*`` to separate keywords in the name of the job, in order. For example: - -- ``1850*fc0*_1_``: List all the jobs that have the string ``1850`` and then at least 1 occurrence of the string ``fc0`` and then at least 1 occurrence of the string ``_1_``. This will effectively list all the jobs for the DATE that starts with ``1850`` for the member ``fc0`` and the chunk ``_1_``. -- ``000*_5``: List all the jobs that have the string ``000`` followed by at least one occurrence of the string ``_5``. This will effectively list all the jobs that have member ``000`` and chunk number that starts with the digit ``5``. -- ``000*_5*PREPROCVAR``: It will also add the filter for jobs of type ``PREPROCVAR``. - -As you might infer, the logic is fairly straightforward: Start your string with the word or part of the word you are looking for, then add ``*`` and the word or part of the word that follows, and so on. The algorithm will split your string by ``*`` and then search for each part in order, once it finds the part in the title of the job, it takes a substring of the job title to not repeat the next search in the same string, it continues looking for the next part in the new reduced string, and so on. - -You can extend this funcionality considering that date, member, section, chunk names start with the symbol ``_`` and finish with the same symbol. - -.. important:: This view is designed to show a structured view of your experiment, if you want a more dependency oriented view that shows better the execution sequence of your jobs, you can refer to :ref:`graphRepresentation`. - - - diff --git a/docs/build/html/_sources/autosubmit-gui.rst.txt b/docs/build/html/_sources/autosubmit-gui.rst.txt deleted file mode 100644 index 71574f070b74f7a3bfab8b66bc2c7256c643b448..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/autosubmit-gui.rst.txt +++ /dev/null @@ -1,87 +0,0 @@ -Autosubmit GUI -############## - -.. _autosubmitGUIMP: - -Autosubmit GUI Main Page -======================== - -Inside the Barcelona Supercomputing Internal Network you can find the latest version of Autosubmit GUI deployed for BSC users. It can be accessed by following the url http://bscesweb04.bsc.es/autosubmitapp/. This is a graphic user interface that allows you to easily monitor your experiments and those of your colleagues. This Web App introduces many useful features for experiment monitoring, and we are continuously improving it. - -.. note:: The Web App can also be accessed through the VPN Client provided by BSC. - -When you enter the site, you will be presented with the following page: - -.. figure:: /agui/fig1_gui.png - :name: first_page - :width: 100% - :align: center - :alt: autosubmit guide - - Welcome page - -Here you can search for any ongoing or past experiment by typing some text in the Search input box and pressing **Search**: the search engine will look for coincidences between your input string and any of the description, owner or name of the experiment fields. The results will be shown below ordered by status, experiments ``RUNNING`` will be shown in the first rows. You can also click on the ``Running`` button, and all the experiments that are currently running will be listed. The results will look like: - -.. figure:: /agui/fig2_gui.png - :name: first_page_search - :width: 100% - :align: center - :alt: result search - - Search Result - -If you click on ``Show Detailed Data``, summary data for each experiment (result) will be loaded. These are data details from the experiment run, useful to see its status at a glance. Progress bars and status will use different colors to highlight the important information. - -.. figure:: /agui/fig3_gui.png - :name: first_page_search_plus - :width: 100% - :align: center - :alt: result search plus - - Search Result plus Detailed Data - -For each experiment, you see the following data: - -.. figure:: /agui/fig4_gui.jpg - :name: first_page_search_plus_description - :width: 100% - :align: center - :alt: result search plus description - - Description of Detailed Data - -1. *Experiment Name* -2. *Progress Bar*: Shows completed jobs / total jobs. It turns red when there are **failed** jobs in the experiment, but **Show Detailed Data** should have been requested. -3. *Experiment Status*: *RUNNING* or *NOT RUNNING*. -4. *Owner* -5. *Experiment Description* -6. *Refresh button*: It will say *Summary* when the detailed data has not been requested. If it says *Summary* and you click on it, it will load datailed data for that experiment, otherwise it will refresh the existing detailed data. -7. *More button*: Opens the **Experiment Page**. -8. *Average Queue Time* for all jobs. -9. *Average Run Time* for all jobs. -10. *Number of Running Jobs* -11. *Number of Queuing Jobs* -12. *Number of Submitted Jobs* -13. *Number of Suspended Jobs* -14. *Number of Failed Jobs*: If there are Failed jobs, a list of the names of those jobs will be displayed. - -.. figure:: /agui/fig5_gui.jpg - :name: first_page_search_plus_description_sim - :width: 100% - :align: center - :alt: result search plus description + sim - - Average Times Feature - -In experiments that include ``SIM`` jobs, you will also see the average queuing and running time for these jobs. In the latest version the time format has been updated to ``HH:mm:ss``. The text for the ``SIM`` average follows the format ``avg. queue HH:mm:ss (M) | run HH:mm:ss (N)`` where ``M`` is the number of jobs considered for the ``avg. queue`` calculation and ``N`` is the number of jobs considered for ``run`` calculation. - -After clicking on the **MORE** button, you will be presented with the **Experiment Page**, which is the main view that Autosubmit provides. These are its main components: - -.. toctree:: - agui/experiment - agui/tree - agui/graph - agui/log - agui/statistics - -.. important:: To improve response times, Autosubmit GUI will try to store the dependency structure of your experiment in a database filed called ``structure_expid.db`` where ``expid`` is the name of your experiment. This file will be located in ``/esarchive/autosubmit/expid/pkl/``. \ No newline at end of file diff --git a/docs/build/html/_sources/codedoc/autosubmit.rst.txt b/docs/build/html/_sources/codedoc/autosubmit.rst.txt deleted file mode 100644 index 2c62df12df61b083f655ab8f7c7cc1d54c7452c8..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/codedoc/autosubmit.rst.txt +++ /dev/null @@ -1,8 +0,0 @@ -========== -autosubmit -========== -.. automodule:: autosubmit.autosubmit - :show-inheritance: - :inherited-members: - :members: - diff --git a/docs/build/html/_sources/codedoc/config.rst.txt b/docs/build/html/_sources/codedoc/config.rst.txt deleted file mode 100644 index 5fb79db246f54dee7164c59c8ded7b640b005de4..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/codedoc/config.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -autosubmit.config -================= - -autosubmit.config.basicConfig ------------------------------ - -.. automodule:: autosubmit.config.basicConfig - :show-inheritance: - :inherited-members: - :members: - -autosubmit.config.config_common -------------------------------- -.. automodule:: autosubmit.config.config_common - :show-inheritance: - :inherited-members: - :members: - diff --git a/docs/build/html/_sources/codedoc/database.rst.txt b/docs/build/html/_sources/codedoc/database.rst.txt deleted file mode 100644 index 0ad3b06ad195eb1d08be66a954c52f2a0fd1527e..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/codedoc/database.rst.txt +++ /dev/null @@ -1,4 +0,0 @@ -autosubmit.database -=================== -.. automodule:: autosubmit.database.db_common - :members: diff --git a/docs/build/html/_sources/codedoc/git.rst.txt b/docs/build/html/_sources/codedoc/git.rst.txt deleted file mode 100644 index ba32da717ea490a7bbdfc67b72186bf18381f34e..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/codedoc/git.rst.txt +++ /dev/null @@ -1,4 +0,0 @@ -autosubmit.git -============== -.. automodule:: autosubmit.git.autosubmit_git - :members: diff --git a/docs/build/html/_sources/codedoc/job.rst.txt b/docs/build/html/_sources/codedoc/job.rst.txt deleted file mode 100644 index 16e9ab95add9043c0a6e05c72c4618dd330157a1..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/codedoc/job.rst.txt +++ /dev/null @@ -1,8 +0,0 @@ -autosubmit.job -============== -.. automodule:: autosubmit.job.job - :members: -.. automodule:: autosubmit.job.job_common - :members: -.. automodule:: autosubmit.job.job_list - :members: \ No newline at end of file diff --git a/docs/build/html/_sources/codedoc/main.rst.txt b/docs/build/html/_sources/codedoc/main.rst.txt deleted file mode 100644 index 737c0d767bc130ca400a67edf718f541987abb4f..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/codedoc/main.rst.txt +++ /dev/null @@ -1,14 +0,0 @@ -******************** -Module documentation -******************** - -.. toctree:: - :titlesonly: - - autosubmit - config - database - git - job - monitor - platforms \ No newline at end of file diff --git a/docs/build/html/_sources/codedoc/monitor.rst.txt b/docs/build/html/_sources/codedoc/monitor.rst.txt deleted file mode 100644 index f6819f2d7fd7e5ffbaecd54f6a5c2d7ef63baff3..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/codedoc/monitor.rst.txt +++ /dev/null @@ -1,4 +0,0 @@ -autosubmit.monitor -================== -.. automodule:: autosubmit.monitor.monitor - :members: diff --git a/docs/build/html/_sources/codedoc/platforms.rst.txt b/docs/build/html/_sources/codedoc/platforms.rst.txt deleted file mode 100644 index 4fb9f3ee98df659373dd4df147cb7a55ca3d795f..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/codedoc/platforms.rst.txt +++ /dev/null @@ -1,22 +0,0 @@ -autosubmit.platform -=================== -.. automodule:: autosubmit.platforms.ecplatform - :show-inheritance: - :members: -.. automodule:: autosubmit.platforms.lsfplatform - :show-inheritance: - :members: -.. automodule:: autosubmit.platforms.pbsplatform - :show-inheritance: - :members: -.. automodule:: autosubmit.platforms.sgeplatform - :show-inheritance: - :members: -.. automodule:: autosubmit.platforms.slurmplatform - :show-inheritance: - :members: -.. automodule:: autosubmit.platforms.locplatform - :show-inheritance: - :members: - - diff --git a/docs/build/html/_sources/faq.rst.txt b/docs/build/html/_sources/faq.rst.txt deleted file mode 100644 index abc03240c429e9c207f31590ae3d88b78ffdd34b..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/faq.rst.txt +++ /dev/null @@ -1,135 +0,0 @@ -############ -FAQ - Frequently Asked Questions -############ - -[CRITICAL] Unhandled exception on Autosubmit: [Errno 11] Resource temporarily unavailable -==================== - -.. code-block:: python - - [CRITICAL] Unhandled exception on Autosubmit: [Errno 11] Resource temporarily unavailable - Traceback (most recent call last): - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/autosubmit.py", line 402, in parse_args - args.group_by, args.expand, args.expand_status) - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/autosubmit.py", line 2093, in set_status - with portalocker.Lock(os.path.join(tmp_path, 'autosubmit.lock'), timeout=1): - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/portalocker-1.2.0-py2.7.egg/portalocker/utils.py", line 195, in __enter__ - return self.acquire() - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/portalocker-1.2.0-py2.7.egg/portalocker/utils.py", line 155, in acquire - raise exceptions.LockException(exception) - LockException: [Errno 11] Resource temporarily unavailable - - -Solution ---------------- -Make sure the experiment is not still running. If it's not, delete the autosubmit.lock in the /tmp folder inside your experiment directory. - ----- - -[CRITICAL] Unhandled exception on Autosubmit: attempt to write a readonly database -==================== - -.. code-block:: python - - [CRITICAL] Unhandled exception on Autosubmit: attempt to write a readonly database - Traceback (most recent call last): - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/autosubmit - .py", line 389, in parse_args - return Autosubmit.create(args.expid, args.noplot, args.hide, args.output, args.group_by, args.expand, args.expand_status) - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/autosubmit - .py", line 1953, in create - "job_packages_" + expid).reset_table() - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/job/job_pa - ckage_persistence.py", line 65, in reset_table - self.db_manager.drop_table(self.JOB_PACKAGES_TABLE) - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/database/d - b_manager.py", line 65, in drop_table - cursor.execute(drop_command) - OperationalError: attempt to write a readonly database - -Solution ---------------- -This usually happens when trying to run `autosubmit create` with an expid of another user, please double check the expid you are using. - ----- - -[ERROR] Command sbatch -D ... failed with error message: sbatch: error: Batch job submission failed: Invalid account or account/partition combination specified -==================== - -Solution ---------------- -This can be due to an invalid configuration in your ~/.ssh/config file, so check if you are able to run a ssh command using the account displayed in the error message. -If so, once you are in the remote platform, type bsc_acct and see if the information for your username/account is displayed: - -.. code-block:: ini - - USER CONSUMED CPU: - - User:                                             Machine:          Used [khours]: - -If not, contact support referring to the problem and specifying your account. - ----- - -[ERROR] Cannot send file to remote platform -=================================== - -.. code-block:: python - - [ERROR] marenostrum4 submission failed - [CRITICAL] Unhandled exception on Autosubmit: size mismatch in put! 0 != 38998 - Traceback (most recent call last): - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/autosubmit.py", line 368, in parse_args - return Autosubmit.run_experiment(args.expid) - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/autosubmit.py", line 776, in run_experiment - if Autosubmit.submit_ready_jobs(as_conf, job_list, platforms_to_test, packages_persistence): - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/autosubmit.py", line 819, in submit_ready_jobs - package.submit(as_conf, job_list.parameters) - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/job/job_packages.py", line 87, in submit - self._send_files() - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/job/job_packages.py", line 115, in _send_files - self.platform.send_file(self._job_scripts[job.name]) - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/platforms/paramiko_platform.py", line 129, in send_file - ftp.put(os.path.join(self.tmp_path, filename), os.path.join(self.get_files_path(), filename)) - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/paramiko-1.15.0-py2.7.egg/paramiko/sftp_client.py", line 669, in put - return self.putfo(fl, remotepath, file_size, callback, confirm) - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/paramiko-1.15.0-py2.7.egg/paramiko/sftp_client.py", line 635, in putfo - raise IOError('size mismatch in put! %d != %d' % (s.st_size, size)) - IOError: size mismatch in put! 0 != 38998 - -This happens when the quota has been reached and the machine is full - ----- - -[CRITICAL] Unhandled exception on Autosubmit: database is locked -=================================== - -.. code-block:: python - - [CRITICAL] Unhandled exception on Autosubmit: database is locked - Traceback (most recent call last): - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/autosubmit.py", line 377, in parse_args - args.operational) != '' - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/autosubmit.py", line 532, in expid - exp_id = copy_experiment(copy_id, description, Autosubmit.autosubmit_version, test, operational) - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/experiment/experiment_common.py", line 93, in copy_experiment - new_name = new_experiment(description, version, test, operational) - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/experiment/experiment_common.py", line 68, in new_experiment - if not db_common.save_experiment(new_name, description, version): - File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/database/db_common.py", line 151, in save_experiment - {'name': name, 'description': description, 'version': version}) - OperationalError: database is locked - -Solution ---------------- -If you were trying to copy an experiment, make sure you put the -y immediately after expid: `autosubmit expid -y` - ----- - -bash: sbatch: command not found -=================================== - -Solution ---------------- -First, check your jobs_expid.conf and platforms_expid.conf files and make sure the platform assigned to the running job is defined correctly and is a SLURM platform. -If this is ok, check that the hostname of the platform you are using is also correctly defined in your ~/.ssh/config file. diff --git a/docs/build/html/_sources/index.rst.txt b/docs/build/html/_sources/index.rst.txt deleted file mode 100644 index 54bbff9600d061fc7d5e9390257689c7c292f5c4..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/index.rst.txt +++ /dev/null @@ -1,25 +0,0 @@ -.. autosubmit documentation master file, created by - sphinx-quickstart on Wed Mar 18 16:55:44 2015. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -###################################### -Welcome to autosubmit's documentation! -###################################### - -.. toctree:: - :titlesonly: - :maxdepth: 5 - - introduction - tutorial - installation - usage - workflows - troubleshoot - faq - project - variables - codedoc/main - autosubmit-gui - diff --git a/docs/build/html/_sources/installation.rst.txt b/docs/build/html/_sources/installation.rst.txt deleted file mode 100644 index 90a931b69b40b9dedd74ddd898c1a03e41a76c46..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/installation.rst.txt +++ /dev/null @@ -1,71 +0,0 @@ -############ -Installation -############ - -How to install -============== - -The Autosubmit code is maintained in *PyPi*, the main source for python packages. - -- Pre-requisties: These packages (bash, python2, sqlite3, git-scm > 1.8.2, subversion, dialog and GraphViz) must be available at local host machine. - -These packages (argparse, python-dateutil, pyparsing, numpy, pydotplus, matplotlib, paramiko,python2-pythondialog and portalocker) must be available for python runtime. - -.. important:: The host machine has to be able to access HPC's/Clusters via password-less ssh. - -To install autosubmit just execute: -:: - - pip install autosubmit - -or download, unpack and: -:: - - python setup.py install - -.. hint:: - To check if autosubmit has been installed run ``autosubmit -v.`` This command will print autosubmit's current - version - -.. hint:: - To read autosubmit's readme file, run ``autosubmit readme`` - -.. hint:: - To see the changelog, use ``autosubmit changelog`` - -How to configure -================ - -After installation, you have to configure database and path for Autosubmit. -In order to use the default settings, just create a directory called `autosubmit` in your home directory before running the configure command. -The experiments will be created in this folder, and the database named `autosubmit.db` in your home directory. - -:: - - autosubmit configure - - - - -For advanced options you can add `--advanced` to the configure command. It will allow you to choose different directories (they must exist) for the experiments and database, -as well as configure SMTP server and an email account in order to use the email notifications feature. - - -:: - - autosubmit configure --advanced - - -.. hint:: - The ``dialog`` (GUI) library is optional. Otherwise the configuration parameters - will be prompted (CLI). Use ``autosubmit configure -h`` to see all the allowed options. - - -For installing the database for Autosubmit on the configured folder, when no database is created on the given path, execute: -:: - - autosubmit install - -.. danger:: Be careful ! autosubmit install will create a blank database. - -Now you are ready to use Autosubmit ! diff --git a/docs/build/html/_sources/introduction.rst.txt b/docs/build/html/_sources/introduction.rst.txt deleted file mode 100644 index 14b9f82f1dd650db4443e748af1eadb45204410b..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/introduction.rst.txt +++ /dev/null @@ -1,116 +0,0 @@ -############ -Introduction -############ - -What is Autosubmit ? -==================== - -Autosubmit is a python-based tool to create, manage and monitor experiments by using Computing Clusters, HPC's and -Supercomputers remotely via ssh. It has support for experiments running in more than one HPC and for different workflow -configurations. - -Autosubmit is currently used at Barcelona Supercomputing Centre (BSC) to run EC-Earth, NEMO and NMMB air quality model. - -Autosubmit has been used to manage models running at supercomputers in IC3, BSC, ECMWF, EPCC, PDC and OLCF. - -Autosubmit is now available via *PyPi* package under the terms of *GNU General Public License*. - -+----------------------------------------------------------------------+ -| Get involved or contact us: | -+==========================+===========================================+ -| Autosubmit GitLab: | https://earth.bsc.es/gitlab/es/autosubmit | -+--------------------------+-------------------------------------------+ -| Autosubmit Mailing List: | autosubmit@bsc.es | -+--------------------------+-------------------------------------------+ - -Why is Autosubmit needed ? -========================== - -Autosubmit is the only existing tool that satisfies the following requirements from the weather and climate community: - -- *Automatisation*: Job submission to machines and dependencies between jobs are managed by Autosubmit. No user intervention is needed. -- *Data provenance*: Assigns unique identifiers for each experiment and stores information about model version, experiment configuration and computing facilities used in the whole process. -- *Failure tolerance*: Automatic retrials and ability to rerun chunks in case of corrupted or missing data. -- *Resource management*: Autosubmit manages supercomputer particularities, allowing users to run their experiments in the available machine without having to adapt the code. Autosubmit also allows to submit tasks from the same experiment to different platforms. - - -How does Autosubmit work ? -========================== - -You can find help about how to use autosubmit and a list of available commands, just executing: -:: - - autosubmit -h - -Execute autosubmit -h for detailed help for each command: -:: - - autosubmit expid -h - -Experiment creation -------------------- - -To create a new experiment, run the command: -:: - - autosubmit expid -H HPCname -d Description - -*HPCname* is the name of the main HPC platform for the experiment: it will be the default platform for the tasks. -*Description* is a brief experiment description. - -This command assigns a unique four character identifier (``xxxx``, names starting from a letter, the other three characters) to the experiment and creates a new folder in experiments repository with structure shown in Figure :numref:`exp_folder`. - -.. figure:: fig1.png - :name: exp_folder - :width: 33% - :align: center - :alt: experiment folder - - Example of an experiment directory tree. - -Experiment configuration ------------------------- - -To configure the experiment, edit ``expdef_xxxx.conf``, ``jobs_xxxx.conf`` and ``platforms_xxxx.conf`` in the ``conf`` folder of the experiment (see contents in Figure :numref:`exp_config`). - -.. figure:: fig2.png - :name: exp_config - :width: 50% - :align: center - :alt: configuration files - - Configuration files content - -After that, you are expected to run the command: -:: - - autosubmit create xxxx - -This command creates the experiment project in the ``proj`` folder. The experiment project contains the scripts specified in ``jobs_xxxx.conf`` and a copy of model source code and data specified in ``expdef_xxxx.conf``. - -Experiment run --------------- - -To run the experiment, just execute the command: - -:: - - autosubmit run xxxx - -Autosubmit will start submitting jobs to the relevant platforms (both HPC and supporting computers) by using the scripts specified in ``jobs_xxxx.conf``. Autosubmit will substitute variables present on scripts where handlers appear in *%variable_name%* format. Autosubmit provides variables for *current chunk*, *start date*, *member*, *computer configuration* and more, and also will replace variables form ``proj_xxxx.conf``. - -To monitor the status of the experiment, the command: - -:: - - autosubmit monitor xxxx - -is available. This will plot the workflow of the experiment and the current status. - -.. figure:: fig3.png - :width: 70% - :align: center - :alt: experiment plot - - Example of monitoring plot for EC-Earth run with Autosubmit for 1 start date, 1 member and 3 chunks. - diff --git a/docs/build/html/_sources/project.rst.txt b/docs/build/html/_sources/project.rst.txt deleted file mode 100644 index 6c91991c14cbe5dea27b65c4db4f0d5e096aa437..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/project.rst.txt +++ /dev/null @@ -1,34 +0,0 @@ -#################### -Developing a project -#################### - -Autosubmit is used at BSC to run EC-Earth. To do that, a git repository has been created that contains the model source -code and the scripts used to run the tasks. - -.. figure:: fig3.png - :width: 70% - :align: center - :alt: EC-Earth experiment - - Example of monitoring plot for EC-Earth run with Autosubmit for 1 start date, 1 member and 3 chunks. - -The workflow is defined using seven job types, as shown in the figure above. These job types are: - -- Local_setup: prepares a patch for model changes and copies it to HPC. -- Remote_setup: creates a model copy and applies the patch to it. -- Ini: prepares model to start the simulation of one member. -- Sim: runs a simulation chunk (usually 1 to 3 months). -- Post: post-process outputs for one simulation chunk. -- Clean: removes unnecessary outputs from the simulated chunk. -- Transfer: transfers post-processed outputs to definitive storage. - -Since Autosubmit 2.2 the user can select the desired source repository for the experiment project and using a given concrete branch is possible. -This introduce a better version control system for project and more options to create new experiments based on different developments by the user. -The different projects contain the shell script to run, for each job type (local setup, remote setup, ini, sim, post, clean and transfer) that are platform independent. -Additionally the user can modify the sources under proj folder. -The executable scripts are created at runtime so the modifications on the sources can be done on the fly. - -.. warning:: Autosubmit automatically adds small shell script code blocks in the header and the tailer of your scripts, to control the workflow. - Please, remove any exit command in the end of your scripts, e.g. ``exit 0``. - -.. important:: For a complete reference on how to develop an EC-Earth project, please have a look in the following wiki page: https://earth.bsc.es/wiki/doku.php?id=models:models \ No newline at end of file diff --git a/docs/build/html/_sources/troubleshoot.rst.txt b/docs/build/html/_sources/troubleshoot.rst.txt deleted file mode 100644 index 60d4071a5b9c87e5084f16be47d8075dd0183ca5..0000000000000000000000000000000000000000 --- a/docs/build/html/_sources/troubleshoot.rst.txt +++ /dev/null @@ -1,133 +0,0 @@ -############### -Troubleshooting -############### - -How to change the job status stopping autosubmit -================================================ - -This procedure allows you to modify the status of your jobs. - -.. warning:: Beware that Autosubmit must be stopped to use ``setstatus``. - Otherwise a running instance of Autosubmit, at some point, will overwritte any change you may have done. - -You must execute: -:: - - autosubmit setstatus EXPID -fs STATUS_ORIGINAL -t STATUS_FINAL -s - -*EXPID* is the experiment identifier. -*STATUS_ORIGINAL* is the original status to filter by the list of jobs. -*STATUS_FINAL* the desired target status. - -Options: -:: - - usage: autosubmit setstatus [-h] [-np] [-s] -t - {READY,COMPLETED,WAITING,SUSPENDED,FAILED,UNKNOWN,QUEUING,RUNNING} - (-fl LIST - | -fc FILTER_CHUNKS - | -fs {Any,READY,COMPLETED,WAITING,SUSPENDED,FAILED,UNKNOWN} - | -ft FILTER_TYPE) - [--hide] - expid - - expid experiment identifier - -h, --help show this help message and exit - -np, --noplot omit plot - -s, --save Save changes to disk - -t {READY,COMPLETED,WAITING,SUSPENDED,FAILED,UNKNOWN}, - --status_final {READY,COMPLETED,WAITING,SUSPENDED,FAILED,UNKNOWN} - Supply the target status - -fl LIST, --list LIST Supply the list of job names to be changed. Default = - "Any". LIST = "cxxx_20101101_fc3_21_sim - cxxx_20111101_fc4_26_sim" - -fc FILTER_CHUNKS, --filter_chunks FILTER_CHUNKS - Supply the list of chunks to change the status. - Default = "Any". LIST = "[ 19601101 [ fc0 [1 2 3 4] - fc1 [1] ] 19651101 [ fc0 [16-30] ] ]" - -fs {Any,READY,COMPLETED,WAITING,SUSPENDED,FAILED,UNKNOWN}, - --filter_status {Any,READY,COMPLETED,WAITING,SUSPENDED,FAILED,UNKNOWN} - Select the original status to filter the list of jobs - -ft FILTER_TYPE, --filter_type FILTER_TYPE - Select the job type to filter the list of jobs - -Examples: -:: - - autosubmit setstatus cxxx -fl "cxxx_20101101_fc3_21_sim cxxx_20111101_fc4_26_sim" -t READY -s - autosubmit setstatus cxxx -fc "[ 19601101 [ fc1 [1] ] ]" -t READY -s - autosubmit setstatus cxxx -fs FAILED -t READY -s - autosubmit setstatus cxxx -ft TRANSFER -t SUSPENDED -s - -This script has two mandatory arguments. - -The -t where you must specify the target status of the jobs you want to change to: -:: - - {READY,COMPLETED,WAITING,SUSPENDED,FAILED,UNKNOWN} - - -The second argument has four alternatives, the -fl, -fc, -fs and -ft; with those we can apply a filter for the jobs we want to change: - -* The -fl variable recieves a list of jobnames separated by blank spaces: e.g.: - :: - - "cxxx_20101101_fc3_21_sim cxxx_20111101_fc4_26_sim" - -If we supply the key word "Any", all jobs will be changed to the target status. - -* The variable -fc should be a list of individual chunks or ranges of chunks in the following format: - :: - - [ 19601101 [ fc0 [1 2 3 4] fc1 [1] ] 19651101 [ fc0 [16-30] ] ] - -* The variable -fs can be the following status for job: - :: - - {Any,READY,COMPLETED,WAITING,SUSPENDED,FAILED,UNKNOWN} - -* The variable -ft can be one of the defined types of job. - -.. hint:: When we are satisfied with the results we can use the parameter -s, which will save the change to the pkl file. - -How to change the job status without stopping autosubmit -======================================================== - - This procedure allows you to modify the status of your jobs without having to stop Autosubmit. - -You must create a file in ``//pkl/`` named: -:: - - updated_list_.txt - -Format: - -This file should have two columns: the first one has to be the job_name and the second one the status. - -Options: -:: - - READY,COMPLETED,WAITING,SUSPENDED,FAILED,UNKNOWN - -Example: -:: - - vi updated_list_cxxx.txt - -.. code-block:: ini - - cxxx_20101101_fc3_21_sim READY - cxxx_20111101_fc4_26_sim READY - -If Autosubmit finds the above file, it will process it. You can check that the processing was OK at a given date and time, -if you see that the file name has changed to: -:: - - update_list___