Before You Start: Known Bugs in ParaDiS - Revision history

Nbertin at 23:03, 27 April 2017

2017-04-27T23:03:37Z

Caiwei at 17:56, 2 April 2013

2013-04-02T17:56:41Z

← Older revision		Revision as of 17:56, 2 April 2013
Line 16:		Line 16:

	If your computer does not allow opening of X-window, then you need to set <tt>enable_window = 0</tt> in your <tt>win.script</tt> file. This is also necessary if you submit your job to a queue in a cluster, because you won't be able to open an interactive window there.		If your computer does not allow opening of X-window, then you need to set <tt>enable_window = 0</tt> in your <tt>win.script</tt> file. This is also necessary if you submit your job to a queue in a cluster, because you won't be able to open an interactive window there.


	== Bug 2. Cell ownership ==		== Bug 2. Cell ownership ==
Line 26:		Line 27:
	results should be insignificant, but on small simulations with very few		results should be insignificant, but on small simulations with very few
	dislocations, differences are more noticable.		dislocations, differences are more noticable.


	== Bug 3. Gcc with v2.3.5 ==		== Bug 3. Gcc with v2.3.5 ==
Line 47:		Line 49:
	#5 0x000000000040185a in main ()		#5 0x000000000040185a in main ()
	</pre></blockquote>		</pre></blockquote>


	== Bug 4. Segfault with X-window ==		== Bug 4. Segfault with X-window ==
	Not really a bug, but a suggestion. When an X-window cannot be opened sucessfully the code exits with a segmentation fault. Should be able to add a descriptive message and a break instead.		Not really a bug, but a suggestion. When an X-window cannot be opened sucessfully the code exits with a segmentation fault. Should be able to add a descriptive message and a break instead.


	== Bug 5. Input files created in DOS system ==		== Bug 5. Input files created in DOS system ==

Caiwei: /* Bug 6. makefile.setup */

2013-04-02T17:49:42Z

Bug 6. makefile.setup

← Older revision		Revision as of 17:49, 2 April 2013
Line 88:		Line 88:


	== Bug 6. makefile.setup ==		== Bug 6. White space in makefile.setup ==

	Make sure there is no white space after your specification of the 'SYS' variable, e.g.		Make sure there is no white space after your specification of the 'SYS' variable, e.g.

Caiwei at 17:46, 2 April 2013

2013-04-02T17:46:55Z

← Older revision		Revision as of 17:46, 2 April 2013
Line 1:		Line 1:
	== Bug 1 ==		== Bug 1. Serial mode in v2.0 ==

	If you download the standard distribution of ParaDiS <tt>pub-dd3d.v2.0.tar.gz</tt>, you will not be able to compile and run it in SERIAL mode. The fix to this problem is described below.		If you download the standard distribution of ParaDiS <tt>pub-dd3d.v2.0.tar.gz</tt>, you will not be able to compile and run it in SERIAL mode. The fix to this problem is described below.
Line 17:		Line 17:
	If your computer does not allow opening of X-window, then you need to set <tt>enable_window = 0</tt> in your <tt>win.script</tt> file. This is also necessary if you submit your job to a queue in a cluster, because you won't be able to open an interactive window there.		If your computer does not allow opening of X-window, then you need to set <tt>enable_window = 0</tt> in your <tt>win.script</tt> file. This is also necessary if you submit your job to a queue in a cluster, because you won't be able to open an interactive window there.

	== Bug 2 ==		== Bug 2. Cell ownership ==
	As the numbers of		As the numbers of
	cells and numbers of processors are changed, ownership or nodes/segments can		cells and numbers of processors are changed, ownership or nodes/segments can
Line 27:		Line 27:
	dislocations, differences are more noticable.		dislocations, differences are more noticable.

	== Bug 3 ==		== Bug 3. Gcc with v2.3.5 ==
	Segmentation fault occurs with v2.3.5s and v.2.3.5.1 when compiling with GCC on Ubuntu and running codes with FMM. The error when compiling using <tt>-03</tt> optimization in serial or parallel (<tt>cc -O3</tt> or <tt>mpicc -03</tt>). Appears to be specific to <tt>-03</tt> and doesn't occur for <tt>-02</tt> or <tt>-g</tt>, for example. <tt>-03</tt> works properly when using Rijm tables.		Segmentation fault occurs with v2.3.5s and v.2.3.5.1 when compiling with GCC on Ubuntu and running codes with FMM. The error when compiling using <tt>-03</tt> optimization in serial or parallel (<tt>cc -O3</tt> or <tt>mpicc -03</tt>). Appears to be specific to <tt>-03</tt> and doesn't occur for <tt>-02</tt> or <tt>-g</tt>, for example. <tt>-03</tt> works properly when using Rijm tables.

Line 48:		Line 48:
	</pre></blockquote>		</pre></blockquote>

	== Bug 4 ==		== Bug 4. Segfault with X-window ==
	Not really a bug, but a suggestion. When an X-window cannot be opened sucessfully the code exits with a segmentation fault. Should be able to add a descriptive message and a break instead.		Not really a bug, but a suggestion. When an X-window cannot be opened sucessfully the code exits with a segmentation fault. Should be able to add a descriptive message and a break instead.

	== Bug 5. ~~Errors of input~~ files created in a DOS system ==		== Bug 5. Input files created in DOS system ==
	When ParaDiS input files (control and data files) are created in a DOS system (MS-DOS or Windows), the input files sometimes cannot be executed even though the files look okay in your editor of your linux system. For example, when you create input files using 'create_dislocation.f' in your DOS (or Windows) system, the hidden character, which is ^M, is embedded at the end of each line in your files. This character is sometimes shown or not shown in your editor. If it is shown, the input files look as the following.		When ParaDiS input files (control and data files) are created in a DOS system (MS-DOS or Windows), the input files sometimes cannot be executed even though the files look okay in your editor of your linux system. For example, when you create input files using 'create_dislocation.f' in your DOS (or Windows) system, the hidden character, which is ^M, is embedded at the end of each line in your files. This character is sometimes shown or not shown in your editor. If it is shown, the input files look as the following.

Line 86:		Line 86:

	We can remove this hidden character ^Ms simply using the command "<tt>dos2unix</tt>". This command erase all ^Ms in your files. Just run <tt>dos2unix (your-input-file-name)</tt>, Then, the input files can be executed.		We can remove this hidden character ^Ms simply using the command "<tt>dos2unix</tt>". This command erase all ^Ms in your files. Just run <tt>dos2unix (your-input-file-name)</tt>, Then, the input files can be executed.


			== Bug 6. makefile.setup ==

			Make sure there is no white space after your specification of the 'SYS' variable, e.g.

			SYS = gcc

			If there is a white space following gcc then the code won't compile.

Swlee49: /* Bug 5 */

2011-05-19T13:57:59Z

Bug 5

← Older revision		Revision as of 13:57, 19 May 2011
Line 51:		Line 51:
	Not really a bug, but a suggestion. When an X-window cannot be opened sucessfully the code exits with a segmentation fault. Should be able to add a descriptive message and a break instead.		Not really a bug, but a suggestion. When an X-window cannot be opened sucessfully the code exits with a segmentation fault. Should be able to add a descriptive message and a break instead.

			== Bug 5. Errors of input files created in a DOS system ==
	== Bug 5 ==
	When ParaDiS input files (control and data files) are created in a DOS system (MS-DOS or Windows), the input files sometimes cannot be executed even though the files look okay in your editor of your linux system. For example, when you create input files using 'create_dislocation.f' in your DOS (or Windows) system, the hidden character, which is ^M, is embedded at the end of each line in your files. This character is sometimes shown or not shown in your editor. If it is shown, the input files look as the following.		When ParaDiS input files (control and data files) are created in a DOS system (MS-DOS or Windows), the input files sometimes cannot be executed even though the files look okay in your editor of your linux system. For example, when you create input files using 'create_dislocation.f' in your DOS (or Windows) system, the hidden character, which is ^M, is embedded at the end of each line in your files. This character is sometimes shown or not shown in your editor. If it is shown, the input files look as the following.

Swlee49 at 13:55, 19 May 2011

2011-05-19T13:55:51Z

← Older revision		Revision as of 13:55, 19 May 2011
Line 50:		Line 50:
	== Bug 4 ==		== Bug 4 ==
	Not really a bug, but a suggestion. When an X-window cannot be opened sucessfully the code exits with a segmentation fault. Should be able to add a descriptive message and a break instead.		Not really a bug, but a suggestion. When an X-window cannot be opened sucessfully the code exits with a segmentation fault. Should be able to add a descriptive message and a break instead.

			== Bug 5 ==
			When ParaDiS input files (control and data files) are created in a DOS system (MS-DOS or Windows), the input files sometimes cannot be executed even though the files look okay in your editor of your linux system. For example, when you create input files using 'create_dislocation.f' in your DOS (or Windows) system, the hidden character, which is ^M, is embedded at the end of each line in your files. This character is sometimes shown or not shown in your editor. If it is shown, the input files look as the following.

			<blockquote style="background: white; border: 0; padding: rem; width: 625px;"><pre>
			### ParaDis nodal file (create_dislocation.f)^M
			### S.A. (10/29/07)###^M
			^M
			#File version number^M
			2^M
			^M
			#Number of data file segments^M
			1^M
			#Minimum coordinate values (x, y, z)^M
			-18348.6238532110 -18348.6238532110 -18348.6238532110^M
			#Maximum coordinate values (x, y, z)^M
			18348.6238532110 18348.6238532110 18348.6238532110^M
			^M
			#Node count^M
			54^M
			#Domain geometry (x, y, z)^M
			1 1 1^M
			...
			...
			</pre></blockquote>

			When the character ^M is not shown, it is frustrating because the input files look perfect, ParaDiS canot execute these inputs with ^Ms and shows the errors such as

			<blockquote style="background: white; border: 0; padding: rem; width: 625px;"><pre>
			...
			Error: Expected '=' in parameter assignment
			Fatal: Error obtaining values for parameter ) is produced.
			...
			</pre></blockquote>

			We can remove this hidden character ^Ms simply using the command "<tt>dos2unix</tt>". This command erase all ^Ms in your files. Just run <tt>dos2unix (your-input-file-name)</tt>, Then, the input files can be executed.

Wcash at 02:46, 11 May 2010

2010-05-11T02:46:41Z

← Older revision		Revision as of 02:46, 11 May 2010
Line 31:		Line 31:

	This doesn't occur with the older version of ParaDiS in the subversion (~2.2.3 or 2.2.6?).		This doesn't occur with the older version of ParaDiS in the subversion (~2.2.3 or 2.2.6?).

			Details of error:
			<blockquote style="background: white; border: 0; padding: rem; width: 625px;"><pre>
			Initialize: Control file parsing complete
			Generating uniform domain decomposition.

			Program received signal SIGSEGV, Segmentation fault.
			0x00007ffff732896d in ?? () from /lib/libc.so.6
			(gdb) backtrace
			#0 0x00007ffff732896d in ?? () from /lib/libc.so.6
			#1 0x00007ffff732b424 in calloc () from /lib/libc.so.6
			#2 0x0000000000448911 in ReadNodeDataFile ()
			#3 0x000000000042dcd4 in Initialize ()
			#4 0x000000000040e321 in ParadisInit ()
			#5 0x000000000040185a in main ()
			</pre></blockquote>

	== Bug 4 ==		== Bug 4 ==

Wcash: added GCC bug for 2.3.5s and 2.3.5.1

2010-05-11T00:44:48Z

added GCC bug for 2.3.5s and 2.3.5.1

← Older revision		Revision as of 00:44, 11 May 2010
Line 26:		Line 26:
	results should be insignificant, but on small simulations with very few		results should be insignificant, but on small simulations with very few
	dislocations, differences are more noticable.		dislocations, differences are more noticable.

			== Bug 3 ==
			Segmentation fault occurs with v2.3.5s and v.2.3.5.1 when compiling with GCC on Ubuntu and running codes with FMM. The error when compiling using <tt>-03</tt> optimization in serial or parallel (<tt>cc -O3</tt> or <tt>mpicc -03</tt>). Appears to be specific to <tt>-03</tt> and doesn't occur for <tt>-02</tt> or <tt>-g</tt>, for example. <tt>-03</tt> works properly when using Rijm tables.

			This doesn't occur with the older version of ParaDiS in the subversion (~2.2.3 or 2.2.6?).

			== Bug 4 ==
			Not really a bug, but a suggestion. When an X-window cannot be opened sucessfully the code exits with a segmentation fault. Should be able to add a descriptive message and a break instead.

Saubry: Add a new "bug"

2009-11-23T18:53:26Z

Add a new "bug"

← Older revision		Revision as of 18:53, 23 November 2009
Line 1:		Line 1:
			== Bug 1 ==

	If you download the standard distribution of ParaDiS <tt>pub-dd3d.v2.0.tar.gz</tt>, you will not be able to compile and run it in SERIAL mode. The fix to this problem is described below.		If you download the standard distribution of ParaDiS <tt>pub-dd3d.v2.0.tar.gz</tt>, you will not be able to compile and run it in SERIAL mode. The fix to this problem is described below.

Line 14:		Line 16:

	If your computer does not allow opening of X-window, then you need to set <tt>enable_window = 0</tt> in your <tt>win.script</tt> file. This is also necessary if you submit your job to a queue in a cluster, because you won't be able to open an interactive window there.		If your computer does not allow opening of X-window, then you need to set <tt>enable_window = 0</tt> in your <tt>win.script</tt> file. This is also necessary if you submit your job to a queue in a cluster, because you won't be able to open an interactive window there.

			== Bug 2 ==
			As the numbers of
			cells and numbers of processors are changed, ownership or nodes/segments can
			alter which may result in segments changing the cells into which they
			are accounted... and hence alter results. So for a small test case, forces may be perfectly correct in serial but slightly off in parallel using cells (option FULL_N2Forces turned off).

			On a large simulation the
			results should be insignificant, but on small simulations with very few
			dislocations, differences are more noticable.

Caiwei at 00:14, 20 December 2007

2007-12-20T00:14:32Z

← Older revision		Revision as of 00:14, 20 December 2007
Line 1:		Line 1:
	If you download the standard distribution of ParaDiS <tt>pub-dd3d.v2.0.tar.gz</tt>, you will not be able to compile and run it in SERIAL mode. The fix to this problem is described below.		If you download the standard distribution of ParaDiS <tt>pub-dd3d.v2.0.tar.gz</tt>, you will not be able to compile and run it in SERIAL mode. The fix to this problem is described below.

	You need to download these three files:		You need to download these three files (available on [http://paradis.stanford.edu/downloads ParaDiS download site]):

	~~[[Media:~~ makefile.sys ~~\| makefile.sys]]~~		makefile.sys
			makefile.setup

			ReadConfig.c
	[[Media: makefile.setup \| makefile.setup]]

	[[Media: ReadConfig.c \| ReadConfig.c]]

	This will allow you to use <tt>SYS = i386</tt> or <tt>SYS = cygwin</tt> and <tt>MODE = SERIAL</tt> in <tt>makefile.setup</tt>.		This will allow you to use <tt>SYS = i386</tt> or <tt>SYS = cygwin</tt> and <tt>MODE = SERIAL</tt> in <tt>makefile.setup</tt>.