Main Page - Revision history

Blewis at 14:26, 25 February 2022

2022-02-25T14:26:09Z

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	* [[Project:Pop-Lab\|Pop-Lab]]		* [[Project:Pop-Lab\|Pop-Lab]]
	* [[Project:Cloud-Computing\|Cloud Computing]]		* [[Project:Cloud-Computing\|Cloud Computing]]
	* [~~[Project~~:~~SummerInternships\|~~Summer Internship ~~Projects]~~]		* [https://cbcb.umd.edu/summer-internships CBCB Summer Internship Program] <br>
	* [[Metagenomics Reading Group (Wed 2pm)]]		* [[Metagenomics Reading Group (Wed 2pm)]]

	~~== People ==~~

	* [[User:ayres\|Daniel Ayres]]
	* [[User:pknut777\|Adam Bazinet]]
	* [[User:irina\|Irina Astrovskaya]]
	* [[User:jpaulson\|Joseph Paulson]]
	* [[User:mpop\|Mihai Pop]]
	* [[User:nelsayed\|Najib El-Sayed]]

	== Getting started ==		== Getting started ==
	If you have just received a new ~~umiacs~~ account through CBCB, follow the instructions on this page to get the basic information you'll need to start working:<br>		If you have just received a new UMIACS account through CBCB, follow the instructions on this page to get the basic information you'll need to start working:<br>
	*[[Getting Started in CBCB]]		*[[Getting Started in CBCB]]
	*[[CBCB Software Modules]]		*[[CBCB Software Modules]]

Blewis at 14:24, 25 February 2022

2022-02-25T14:24:05Z

← Older revision		Revision as of 14:24, 25 February 2022
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	== Seminars ==		== Seminars ==
	* [http://www.cbcb.umd.edu/seminars Regular CBCB seminars (during academic year)] <br>
	* [https://cbcb.umd.edu/research-in-progress Research In Progress (RIPS) schedule] <br>		* [https://cbcb.umd.edu/research-in-progress Research In Progress (RIPS) schedule] <br>
	* [[short_read_sequencing\|Short read sequencing Meeting]] (Fridays at 3pm)

	== Projects ==		== Projects ==

	* [[Project:Pop-Lab\|Pop-Lab]]		* [[Project:Pop-Lab\|Pop-Lab]]
	* [[Project:Hcbravo-lab\|HCBravo Lab]]
	* [[Project:Cloud-Computing\|Cloud Computing]]		* [[Project:Cloud-Computing\|Cloud Computing]]
	* [[Project:SummerInternships\|Summer Internship Projects]]		* [[Project:SummerInternships\|Summer Internship Projects]]

Blewis at 14:23, 25 February 2022

2022-02-25T14:23:08Z

← Older revision		Revision as of 14:23, 25 February 2022
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	== Seminars ==		== Seminars ==
	* [http://www.cbcb.umd.edu/seminars Regular CBCB seminars (during academic year)] <br>		* [http://www.cbcb.umd.edu/seminars Regular CBCB seminars (during academic year)] <br>
	* ~~<a href="~~https://cbcb.umd.edu/research-in-progress~~">[[CBCB:~~Research In Progress (RIPS)]~~] - Research in Progress seminar schedule</a>~~<br>		* [https://cbcb.umd.edu/research-in-progress Research In Progress (RIPS) schedule] <br>
	* [[short_read_sequencing\|Short read sequencing Meeting]] (Fridays at 3pm)		* [[short_read_sequencing\|Short read sequencing Meeting]] (Fridays at 3pm)

Blewis at 14:21, 25 February 2022

2022-02-25T14:21:40Z

← Older revision		Revision as of 14:21, 25 February 2022
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	== Seminars ==		== Seminars ==
	* [http://www.cbcb.umd.edu/seminars Regular CBCB seminars (during academic year)] <br>		* [http://www.cbcb.umd.edu/seminars Regular CBCB seminars (during academic year)] <br>
	* [[CBCB:Research In Progress (RIPS)]] - Research in Progress seminar schedule<br>		* <a href="https://cbcb.umd.edu/research-in-progress">[[CBCB:Research In Progress (RIPS)]] - Research in Progress seminar schedule</a><br>
	* [[short_read_sequencing\|Short read sequencing Meeting]] (Fridays at 3pm)		* [[short_read_sequencing\|Short read sequencing Meeting]] (Fridays at 3pm)

Blewis at 14:19, 25 February 2022

2022-02-25T14:19:27Z

← Older revision		Revision as of 14:19, 25 February 2022
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	== Seminars ==		== Seminars ==
	* [http://www.cbcb.umd.edu/seminars Regular CBCB seminars (during academic year)] <br>		* [http://www.cbcb.umd.edu/seminars Regular CBCB seminars (during academic year)] <br>
	* [[~~Cbcb~~:~~Works-~~In-Progress]] - ~~Works~~ in ~~progress~~ seminar schedule ~~(Summer 2008)~~ <br>		* [[CBCB:Research In Progress (RIPS)]] - Research in Progress seminar schedule<br>
	* [[short_read_sequencing\|Short read sequencing Meeting]] (Fridays at 3pm)		* [[short_read_sequencing\|Short read sequencing Meeting]] (Fridays at 3pm)

Derek: /* IMPORTANT (Read First) */

2021-06-28T19:26:04Z

IMPORTANT (Read First)

← Older revision		Revision as of 19:26, 28 June 2021
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	The CBCB computational infrastructure is a shared resource and we all need to pitch in in order to make sure it works well for all of us. Most importantly, we need to ensure that our disk space and computational resources are used responsibly. The disk space, in particular, is a valuable commodity and thus it is important to pay attention to the following:		The CBCB computational infrastructure is a shared resource and we all need to pitch in in order to make sure it works well for all of us. Most importantly, we need to ensure that our disk space and computational resources are used responsibly. The disk space, in particular, is a valuable commodity and thus it is important to pay attention to the following:
	* There are ~~three~~ types of disk space available (a full list of volumes is available at [https://wiki.umiacs.umd.edu/cbcb-private/index.php/Storage CBCB Storage]) :		* There are two types of disk space available (a full list of volumes is available at [https://wiki.umiacs.umd.edu/cbcb-private/index.php/Storage CBCB Storage]) :
	** Local hard drives (usually mounted as /scratch on the machines that have this resource). These are not backed up, are quite fast (they live physically close to the processor), but can only be 'seen' by the machine where they are mounted and, thus, require data staging in/out (which can take a while)		** Local hard drives (usually mounted as /scratch on the machines that have this resource). These are not backed up, are quite fast (they live physically close to the processor), but can only be 'seen' by the machine where they are mounted and, thus, require data staging in/out (which can take a while)
	** Isilon storage (/fs/cbcb-lab, /fs/cbcb-scratch/*, etc.). This is very fast and very expensive disk and thus a limited resource.		** Isilon storage (/fs/cbcb-lab, /fs/cbcb-scratch/*, etc.). This is very fast and very expensive disk and thus a limited resource.

Derek: /* IMPORTANT (Read First) */

2021-06-28T19:25:43Z

IMPORTANT (Read First)

← Older revision		Revision as of 19:25, 28 June 2021
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	The CBCB computational infrastructure is a shared resource and we all need to pitch in in order to make sure it works well for all of us. Most importantly, we need to ensure that our disk space and computational resources are used responsibly. The disk space, in particular, is a valuable commodity and thus it is important to pay attention to the following:		The CBCB computational infrastructure is a shared resource and we all need to pitch in in order to make sure it works well for all of us. Most importantly, we need to ensure that our disk space and computational resources are used responsibly. The disk space, in particular, is a valuable commodity and thus it is important to pay attention to the following:
	* There are three types of disk space available (a full list of volumes is available at [https://wiki.umiacs.umd.edu/cbcb-private/index.php/Storage CBCB Storage]) :		* There are three types of disk space available (a full list of volumes is available at [https://wiki.umiacs.umd.edu/cbcb-private/index.php/Storage CBCB Storage]) :
	** Local ~~harddrives~~ (usually mounted as /scratch on the machines that have this resource). These are not backed up, are quite fast (they live physically close to the processor), but can only be 'seen' by the machine where they are mounted and, thus, require data staging in/out (which can take a while)		** Local hard drives (usually mounted as /scratch on the machines that have this resource). These are not backed up, are quite fast (they live physically close to the processor), but can only be 'seen' by the machine where they are mounted and, thus, require data staging in/out (which can take a while)
	** ~~Shared 3Par~~ storage (/fs/szasmg, /fs/~~szdata~~/, etc.). This is very fast and very expensive disk and thus a limited resource. Please only use this space to store data temporarily, while you are running some analyses on it. As a rule of thumb, if a file or collection of files of any considerable size have lived on this space for more than 1-2 weeks, they should probably be moved to the attic space (see below)		** Isilon storage (/fs/cbcb-lab, /fs/cbcb-scratch/*, etc.). This is very fast and very expensive disk and thus a limited resource.
	** Attic storage (/fs/szattic*). This is cheaper and ample, but slow and brittle storage. Your data-sets should primarily live here. Due to it's brittleness, the IT department do not recommend you run any analyses directly in this volume, rather you copy the files over to a local harddrive or the 3Par instead, and copy the results back when done.
	* You should remove any temporary results you don't need in the long term as soon as you've generated them, and compress all of the large files. Bzip2 works better than gzip but either should dramatically improve the space requirements, especially for text files such as fasta or fastq.		* You should remove any temporary results you don't need in the long term as soon as you've generated them, and compress all of the large files. Bzip2 works better than gzip but either should dramatically improve the space requirements, especially for text files such as fasta or fastq.
	* You should ensure that your files are owned by the cbcb group and that they have group write permissions for any file stored on the 3Par, especially for all those in /fs/szscratch. This will allow your colleagues to remove files in case the disk runs out of space and you are, for example, on vacation (in which case you shouldn't have any major files sitting around on the 3Par).

	For more information on the CBCB resources see [[Getting Started in CBCB]].		For more information on the CBCB resources see [[Getting Started in CBCB]].


	== Seminars ==		== Seminars ==

Bstacy: /* CBCB Private Wiki */

2019-08-29T15:09:42Z

CBCB Private Wiki

← Older revision		Revision as of 15:09, 29 August 2019
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	== CBCB Private Wiki ==		== CBCB Private Wiki ==
	'''You have to be on the UMIACS VPN to view the private wiki if you are not on campus!!'''		'''You have to be on the UMIACS VPN to view the private wiki if you are not on campus!'''
	*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Main_Page CBCB private wiki]		*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Main_Page CBCB private wiki]
	In addition to this wiki there is also the CBCB private wiki. It contains information internal to CBCB, such as information about how to use the cluster.		In addition to this wiki there is also the CBCB private wiki. It contains information internal to CBCB, such as information about how to use the cluster.

Bstacy at 15:09, 29 August 2019

2019-08-29T15:09:28Z

← Older revision		Revision as of 15:09, 29 August 2019
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			== CBCB Private Wiki ==
			'''You have to be on the UMIACS VPN to view the private wiki if you are not on campus!!'''
			*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Main_Page CBCB private wiki]
			In addition to this wiki there is also the CBCB private wiki. It contains information internal to CBCB, such as information about how to use the cluster.

	== IMPORTANT (Read First) ==		== IMPORTANT (Read First) ==

Adric: /* Getting started */ -- Drop Torque reference

2018-11-16T20:04:05Z

Getting started: -- Drop Torque reference

← Older revision		Revision as of 20:04, 16 November 2018
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	*[[Getting Started in CBCB]]		*[[Getting Started in CBCB]]
	*[[CBCB Software Modules]]		*[[CBCB Software Modules]]
	*[~~[Torque]~~]		*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Slurm Slurm]
	*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Storage CBCB Storage]		*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Storage CBCB Storage]
	*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Compute CBCB Computers]		*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Compute CBCB Computers]
	*[[Communal Software]]		*[[Communal Software]]