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Full Discussion: Error running FORTRAN code
Top Forums Programming Error running FORTRAN code Post 302535151 by LMHmedchem on Thursday 30th of June 2011 01:51:10 AM
Old 06-30-2011
This is probably nothing other than an array, of some other data or control structure, that is not declared as large enough. This is common in Fortran because you have to pre-size everything and hope you leave enough space. Sometines an allocation will be sufficient when a program is first developed, but may need to be increased later. The use of a parameter.dat file is common where you hard code constants with sizes for things that may need to change. Then you use the constant as the array size. You keep them all in one place and well documented so it is easy to change. When you have too many input files, the array boundaries are exceeded and there is a seg fault. You could also be flat running out of ram, especially if this is run on an older machine with limited resources.

There are lots of other possibilities, but those are the most likely since the program runs for smaller input files. Another thing to consider is that one of the input files is malformed. Fortran is unbelievably picky about file formats and such, so if one of your models had an issue and produced improperly formatted output, or no output at all, that could also cause in issue if the specific format problem wasn't trapped out. The best way to evaluate that is to try to find where the process fails, if you can find the location in the specific input file where the app crashes, you can look at it to see if there is a visible issue or not.

It is still unclear to me what the final output of the app is supposed to be. If the input files are text files, you can try to compress them, or post them on another location on the web and post a link. If I have a sample of the two input files that you are trying to merge, and a sample of the expected output, it should not be to difficult to fix. The files do not need to be complete, or actual files, just enough to see what the format should be.

A quick look shows that this seems to be set to open up to 1000 files, after that you will exceed the size of the do loop iterator.

Quote:
Originally Posted by Tytalus
are you opening all files concurrently or sequentially; are you closing each file before reading from the next ?
:-)
This is an important point, it looks like all of the files are closed at once, and if you are keep all of those large files opened, you may indeed be running out of memory. You have you checked you resources while the app is running to see how much available RAM you have?

LMHmedchem

Last edited by LMHmedchem; 06-30-2011 at 03:06 AM..
 

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compress(1)							   User Commands						       compress(1)

NAME
compress, uncompress, zcat - compress, uncompress files or display expanded files SYNOPSIS
compress [-fv] [-b bits] [file...] compress [-cfv] [-b bits] [file] uncompress [-cfv] [file...] zcat [file...] DESCRIPTION
compress The compress utility will attempt to reduce the size of the named files by using adaptive Lempel-Ziv coding. Except when the output is to the standard output, each file will be replaced by one with the extension .Z, while keeping the same ownership modes, change times and mod- ification times. If appending the .Z to the file pathname would make the pathname exceed 1023 bytes, the command will fail. If no files are specified, the standard input will be compressed to the standard output. The amount of compression obtained depends on the size of the input, the number of bits per code, and the distribution of common sub- strings. Typically, text such as source code or English is reduced by 50-60%. Compression is generally much better than that achieved by Huffman coding (as used in pack(1)) and it takes less time to compute. The bits parameter specified during compression is encoded within the compressed file, along with a magic number to ensure that neither decompression of random data nor recompression of compressed data is subsequently allowed. uncompress The uncompress utility will restore files to their original state after they have been compressed using the compress utility. If no files are specified, the standard input will be uncompressed to the standard output. This utility supports the uncompressing of any files produced by compress. For files produced by compress on other systems, uncompress sup- ports 9- to 16-bit compression (see -b). zcat The zcat utility will write to standard output the uncompressed form of files that have been compressed using compress. It is the equiva- lent of uncompress -c. Input files are not affected. OPTIONS
The following options are supported: -c Writes to the standard output; no files are changed and no .Z files are created. The behavior of zcat is identical to that of `uncompress -c'. -f When compressing, forces compression of file, even if it does not actually reduce the size of the file, or if the corresponding file.Z file already exists. If the -f option is not given, and the process is not running in the background, prompts to verify whether an existing file.Z file should be overwritten. When uncompressing, does not prompt for overwriting files. If the -f option is not given, and the process is not running in the background, prompts to verify whether an existing file should be over- written. If the standard input is not a terminal and -f is not given, writes a diagnostic message to standard error and exits with a status greater than 0. -v Verbose. Writes to standard error messages concerning the percentage reduction or expansion of each file. -b bits Sets the upper limit (in bits) for common substring codes. bits must be between 9 and 16 (16 is the default). Lowering the number of bits will result in larger, less compressed files. OPERANDS
The following operand is supported: file A path name of a file to be compressed by compress, uncompressed by uncompress, or whose uncompressed form is written to standard out by zcat. If file is -, or if no file is specified, the standard input will be used. USAGE
See largefile(5) for the description of the behavior of compress, uncompress, and zcat when encountering files greater than or equal to 2 Gbyte ( 2**31 bytes). ENVIRONMENT VARIABLES
See environ(5) for descriptions of the following environment variables that affect the execution of compress, uncompress, and zcat: LANG, LC_ALL, LC_CTYPE, LC_MESSAGES, and NLSPATH. EXIT STATUS
The following error values are returned: 0 Successful completion. 1 An error occurred. 2 One or more files were not compressed because they would have increased in size (and the -f option was not specified). >2 An error occurred. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWesu | +-----------------------------+-----------------------------+ |CSI |Enabled | +-----------------------------+-----------------------------+ |Interface Stability |Standard | +-----------------------------+-----------------------------+ SEE ALSO
ln(1), pack(1), attributes(5), environ(5), largefile(5), standards(5) DIAGNOSTICS
Usage: compress [-fvc] [-b maxbits] [file... ] Invalid options were specified on the command line. Missing maxbits Maxbits must follow -b, or invalid maxbits, not a numeric value. file: not in compressed format The file specified to uncompress has not been compressed. file: compressed with xxbits, can only handle yybits file was compressed by a program that could deal with more bits than the compress code on this machine. Recompress the file with smaller bits. file: already has .Z suffix -- no change The file is assumed to be already compressed. Rename the file and try again. file: already exists; do you wish to overwrite (y or n)? Respond y if you want the output file to be replaced; n if not. uncompress: corrupt input A SIGSEGV violation was detected, which usually means that the input file is corrupted. Compression: xx.xx% Percentage of the input saved by compression. (Relevant only for -v.) - - not a regular file: unchanged When the input file is not a regular file, (such as a directory), it is left unaltered. - - has xx other links: unchanged The input file has links; it is left unchanged. See ln(1) for more information. - - file unchanged No savings are achieved by compression. The input remains uncompressed. filename too long to tack on .Z The path name is too long to append the .Z suffix. NOTES
Although compressed files are compatible between machines with large memory, -b 12 should be used for file transfer to architectures with a small process data space (64KB or less). compress should be more flexible about the existence of the .Z suffix. SunOS 5.10 9 Sep 1999 compress(1)
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