Interactive Sessions with idev ============================== The ``idev`` utility initiates an interactive session on one or more compute nodes so that you can issue commands and run code as if you were doing so on your personal machine. An interactive session is useful for development, as you can quickly compile, run, and validate code. Accessing a single compute node is accomplished by simply executing ``idev`` on any of the TACC systems. Initiating an Interactive Session ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ To learn about the command line options available for ``idev``, use ``idev -help``. .. code-block:: console login1$ idev -help ... OPTION ARGUMENTS DESCRIPTION -A account_name sets account name (default: in .idevrc) -m minutes sets time in minutes (default: 30) -p queue_name sets queue to named queue (default: -p development) -r resource_name sets hardware -t hh:mm:ss sets time to hh:mm:ss (default: 00:30:00) -help [--help ] displays (this) help message -v [--version ] output version information and exit Let's go over some of the most useful ``idev`` command line options that can customize your interactive session: To change the **time** limit to be lesser or greater than the default 30 minutes, users can use the ``-m`` command line option. For example, a user requesting an interactive session for an hour would use the command line option ``-m 60``. To change the **account_name** associated with the interactive session, users can use the ``-A`` command line option. This option is useful for when a user has multiple allocations they belong to. For example, if I have allocations on accounts ``TACC`` and ``Training``, I can use ``-A`` to set the allocation I want to be used like so: ``-A TACC`` or ``-A Training``. To change the **queue** to be different than the default ``development`` queue, users can use the ``-p`` command line option. For example, if a user wants to launch an interactive session on one of Lonestar6's GPU nodes, they would use the command line option ``-p gpu-a100`` or ``-p gpu-a100-dev``. You can learn more about the different queues of Lonestar6 `here `_. Note: For the scope of this section, we will be using the default ``development`` queue. To start a thirty-minute interactive session on a compute node in the development queue with our ``EXAMPLE`` allocation: .. code-block:: console login1$ idev -A EXAMPLE If launch is successful, you will see output that includes the following excerpts: .. code-block:: console ... ----------------------------------------------------------------- Welcome to the Lonestar6 Supercomputer ----------------------------------------------------------------- ... -> After your idev job begins to run, a command prompt will appear, -> and you can begin your interactive development session. -> We will report the job status every 4 seconds: (PD=pending, R=running). -> job status: PD -> job status: R -> Job is now running on masternode= c449-0015...OK ... c449-0015(268)$ Exercise ^^^^^^^^ Let's revisit the job we ran in the previous section. This time, we will be going through each command we entered into ``job.slurm`` interactively. .. code-block:: console c449-0015(268)$ pwd /home1/03439/wallen/IntroToLinuxHPC/Lab04 c449-0015(269)$ ls data job.slurm results vina_job.o864828 .. code-block:: console c449-0015(270)$ echo "starting at:" starting at: c449-0015(271)$ date Mon Jun 29 0X:XX:XX CDT 2020 c449-0015(272)$ module list Currently Loaded Modules: # it is okay if you have loaded modules from past sessions c449-0015(273)$ module use /work/03439/wallen/public/modulefiles c449-0115(275)$ module load autodock_vina/1.2.3 c449-0115(276)$ module list Currently Loaded Modules: 1) intel/17.0.4 2) boost/1.64 3) autodock_vina/1.1.2 #the order in which the modules are listed does not matter c449-0015(277)$ cd data/ c449-0015(278)$ vina --config configuration_file.txt --out ../results/output_ligands.pdbqt ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, Journal of Computational Chemistry 31 (2010) # # 455-461 # # # # DOI 10.1002/jcc.21334 # # # # Please see http://vina.scripps.edu for more information. # ################################################################# Detected 272 CPUs WARNING: at low exhaustiveness, it may be impossible to utilize all CPUs Reading input ... done. Setting up the scoring function ... done. Analyzing the binding site ... done. Using random seed: -31156704 Performing search ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| *************************************************** done. Refining results ... done. mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -12.3 0.000 0.000 2 -11.1 1.223 1.866 3 -11.0 3.000 12.459 4 -10.5 2.268 12.434 5 -10.4 2.272 13.237 6 -10.3 3.146 13.666 7 -10.3 3.553 12.345 8 -10.2 1.827 13.667 9 -9.8 2.608 12.630 Writing output ... done. c449-0015(279)$ echo "ending at:" c449-0015(280)$ date Mon Jun 29 0X:XX:XX CDT 2020 To exit an interactive session, you can use the command ``logout``.