Problem with water program

[Len F. Zaifman]

We are using water on a large sequence ( > 10000000 bases) and aligning
a smaller sequence ( < 1000 bases ) to it.  This is for emboss 1.9.1.

The water manual says:

> Diagnostic Error Messages 
> 
> Uncaught exception
>  Assertion failed
>  raised at ajmem.c:xxx
> 
> 
> Probably means you have run out of memory. Try using supermatcher or matcher if this happens. 

This is on an SGI \Origin with Gigabytes of Ram, so I upped the amount
of memory a single process could use from .5 GB to 2 GB and still got
the same result.

On the SGI I use ssusage to determine real memory usage and the memory
usage didn't change in spite of the above change from        
		kernel memory parameters		real memory use
	rlimit_rss_max = 536870912 (0x20000000) ll	75216 mxrss	 4 4k page size
this is 300 MB of ram
	rlimit_rss_cur = 536870912 (0x20000000) ll 

to

        rlimit_rss_max = 2147483648 (0x80000000) ll	75216 mxrss
        rlimit_rss_cur = 2147483648 (0x80000000) ll

(& yes I rebooted the system to ensure I got the new limits).

So I ran water using par to trace the program and got the detailed
output below. It looks to me like it is failing on opening my output
file My.output. Any comments? By the way, this is a file and directory
where I do have write permission, so it is not that.



15728.339mS(+   22uS)[ 16]       water.dbg( 1807): close(5)		<< this
closes 
						/tools/emboss1.9.1/share/EMBOSS/data/EDNAMAT
					
15728.366mS(+   28uS)[ 16]       water.dbg( 1807): END-close() OK

15728.649mS(+  284uS)[ 16]       water.dbg( 1807): open("MY.output",
O_WRONLY|O_CREAT|O_TRUNC, 0666)15728.760mS(+  109uS)[ 16]      
water.dbg( 1807): END-open() = 5  <<
						This is my outputfile from water specified by -outfile

									
15729.497mS(+  738uS)[ 16]       water.dbg( 1807): write(2, "Uncaught
exception", 18)
15729.545mS(+   47uS)[ 16]       water.dbg( 1807): END-write() = 18
15729.558mS(+   12uS)[ 16]       water.dbg( 1807): write(2, "\n", 1)
15729.622mS(+   65uS)[ 16]       water.dbg( 1807): END-write() = 1
15729.642mS(+   17uS)[ 16]       water.dbg( 1807): write(2, " Assertion
failed", 17)
15729.649mS(+    8uS)[ 16]       water.dbg( 1807): END-write() = 17
15729.655mS(+    6uS)[ 16]       water.dbg( 1807): write(2, "\n", 1)
15729.665mS(+    9uS)[ 16]       water.dbg( 1807): END-write() = 1
15729.686mS(+   20uS)[ 16]       water.dbg( 1807): write(2, " raised at
ajmem.c:167\n", 23)
15729.695mS(+   10uS)[ 16]       water.dbg( 1807): END-write() = 23
15729.700mS(+    4uS)[ 16]       water.dbg( 1807): write(2, "\n", 1)
15729.712mS(+   11uS)[ 16]       water.dbg( 1807): END-write() = 1
15729.853mS(+  140uS)[ 16]       water.dbg( 1807): write(2, "\n   EMBOSS
An error in ajexcep", 58)
15729.893mS(+   40uS)[ 16]       water.dbg( 1807): END-write() = 58
15729.900mS(+    7uS)[ 16]       water.dbg( 1807): write(2, "\n", 1)
15729.955mS(+   55uS)[ 16]       water.dbg( 1807): END-write() = 1
15729.998mS(+   43uS)[ 16]       water.dbg( 1807): prctl(PR_LASTSHEXIT)
15730.005mS(+    6uS)[ 16]       water.dbg( 1807): END-prctl() = 1
15730.048mS(+   44uS)[ 16]       water.dbg( 1807): exit(1)
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