Creating Maps on SmallWorld - Revision history

Frodo: /* Step 5: Restart the Server */ asdf

2024-05-24T20:23:56Z

Step 5: Restart the Server: asdf

← Older revision		Revision as of 20:23, 24 May 2024
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	Again, go to the TomCat manager under applications and click Start once you are finished moving around the map files.		Again, go to the TomCat manager under applications and click Start once you are finished moving around the map files.

	[[Category: ~~SmallWorld~~]]		[[Category:Smallworld]]
	[[Category: NextMove]]		[[Category:NextMove]]

2020-01-09T00:11:27Z

2020-01-09T00:11:05Z

← Older revision		Revision as of 00:11, 9 January 2020
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	==Step 5: Restart the Server==		==Step 5: Restart the Server==
	Again, go to the TomCat manager under applications and click Start once you are finished moving around the map files.		Again, go to the TomCat manager under applications and click Start once you are finished moving around the map files.

			[[Category: SmallWorld]]

2019-07-19T18:35:19Z

Step 3-4 Combined: Rather than concatenating and sorting, merge the map file chunks (assuming they are already sorted)

← Older revision		Revision as of 18:35, 19 July 2019
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	ls $j		ls $j
	LC_ALL=C sort -T /nfs/db5/jyoung -c -u $j		LC_ALL=C sort -T /nfs/db5/jyoung -c -u $j
	done		done

	===Step 3: Copy to SSD and Concatenate===		===Step 3: Copy to SSD and Concatenate===

2019-07-19T18:35:05Z

Step 3-4 Combined: Rather than concatenating and sorting, merge the map file chunks (assuming they are already sorted)

← Older revision		Revision as of 18:35, 19 July 2019
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	for j in <combined_map_name>		for j in <combined_map_name>
	do		do
	ls $j		ls $j
	LC_ALL=C sort -T /nfs/db5/jyoung -c -u $j		LC_ALL=C sort -T /nfs/db5/jyoung -c -u $j
	done		done

2019-07-19T18:34:54Z

Step 3-4 Combined: Rather than concatenating and sorting, merge the map file chunks (assuming they are already sorted)

← Older revision		Revision as of 18:34, 19 July 2019
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	===Step 3-4 Combined: Rather than concatenating and sorting, merge the map file chunks (assuming they are already sorted)===		===Step 3-4 Combined: Rather than concatenating and sorting, merge the map file chunks (assuming they are already sorted)===
	Use the -T option on sort to set the temp directory of your choice. If your file is large enough, the sort command needs scratch space to write temporary files to later merge.		Use the -T option on sort to set the temp directory of your choice. If your file is large enough, the sort command needs scratch space to write temporary files to later merge.

	Adjust the matching in the loop rather than just using *.anon.map if you want to be more specific about the files you are combining		Adjust the matching in the loop rather than just using *.anon.map if you want to be more specific about the files you are combining

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	As suggested in the SmallWorld documentation, you can check if the resulting file is sorted using the sort -c option		As suggested in the SmallWorld documentation, you can check if the resulting file is sorted using the sort -c option
	#!/bin/bash		#!/bin/bash
	for j in <combined_map_name>		for j in <combined_map_name>
	do		do

2019-07-19T18:34:31Z

Step 3-4 Combined: Rather than concatenating and sorting, merge the map file chunks (assuming they are already sorted)

← Older revision		Revision as of 18:34, 19 July 2019
Line 99:		Line 99:
	===Step 3-4 Combined: Rather than concatenating and sorting, merge the map file chunks (assuming they are already sorted)===		===Step 3-4 Combined: Rather than concatenating and sorting, merge the map file chunks (assuming they are already sorted)===
	Use the -T option on sort to set the temp directory of your choice. If your file is large enough, the sort command needs scratch space to write temporary files to later merge.		Use the -T option on sort to set the temp directory of your choice. If your file is large enough, the sort command needs scratch space to write temporary files to later merge.
			Adjust the matching in the loop rather than just using *.anon.map if you want to be more specific about the files you are combining

	#!/bin/bash		#!/bin/bash

2019-07-19T18:33:22Z

@@ Line 96: / Line 96: @@
      awk '{print $1"\t"$2}'  <your file> > <your_file_smi_ID>
 to get only these columns before processing with SmallWorld.
 ===Step 3: Copy to SSD and Concatenate===

2019-07-15T22:29:10Z

Step 2: Processing large SMILES files in SmallWorld GREATER than 1 Billion

← Older revision		Revision as of 22:29, 15 July 2019
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	The sorting is done automatically when you generate the SmallWorld maps in a single step like this.		The sorting is done automatically when you generate the SmallWorld maps in a single step like this.

	==Step 2: Processing large SMILES files in SmallWorld GREATER ~~than~~ 1 Billion==		==Step 2: Processing large SMILES files in SmallWorld GREATER THAN 1 Billion==
	If your SMILES file contains more than 1 billion molecules, I think it is better to split the input in to chunks of 1 billion to avoid waiting too long to get intermediate results in case the job fails for some reason.		If your SMILES file contains more than 1 billion molecules, I think it is better to split the input in to chunks of 1 billion to avoid waiting too long to get intermediate results in case the job fails for some reason.

2019-07-15T22:28:57Z

Step 2: Processing large SMILES files in SmallWorld

← Older revision		Revision as of 22:28, 15 July 2019
Line 77:		Line 77:
	The sorting is done automatically when you generate the SmallWorld maps in a single step like this.		The sorting is done automatically when you generate the SmallWorld maps in a single step like this.

	==Step 2: Processing large SMILES files in SmallWorld==		==Step 2: Processing large SMILES files in SmallWorld GREATER than 1 Billion==
	If your SMILES file contains more than 1 billion molecules, I think it is better to split the input in to chunks of 1 billion to avoid waiting too long to get intermediate results in case the job fails for some reason.		If your SMILES file contains more than 1 billion molecules, I think it is better to split the input in to chunks of 1 billion to avoid waiting too long to get intermediate results in case the job fails for some reason.