On 10/02/2015 05:04 AM, MPI wrote:
> Hi Bob,
>
> I tried. I wrap up all 4,500 ATOM records within
>
> load DATA "mydata"
> ATOM ...
> ATOM ...
> .....
> END "mydata"
>
> It dosen't work in both linux and window boxes. See error below.
>
> Exception: java.lang.OutOfMemoryError thrown from the
> UncaughtExceptionHandler in thread "Thread-2"
>
I observe the same if I start Jmol 14.3.16_2015.09.28 to load the PDB
file of PDB entry 1DEH like this (or without selecting only ATOM and
HETATM lines):
cat pdb1deh.ent | perl -ne 'BEGIN { print "load DATA \"mydata\"\n";} if
($_ =~ /^(ATOM|HETATM)/) { print $_; } END { print "END \"mydata\"\n";
}' | java -jar Jmol.jar -I
The resident memory of Jmol increases up to about 6 GB on my machine
until it runs out of memory. The CPU usage is high.
If I am fast enough befor Jmol becomes too unresponsive I can open the
Java console and see the following error messages:
----------------------------------------------------------
script compiler ERROR: unexpected end of script command
----
load DATA >>>> "mydata
<<<<script compiler ERROR: unexpected end of script command
----
load DATA >>>> "mydata
ATOM 1 N SER A 1 15.489 14.526 2.933 1.00 57.01
N
<<<<script compiler ERROR: unexpected end of script command
----
load DATA >>>> "mydata
ATOM 1 N SER A 1 15.489 14.526 2.933 1.00 57.01
N
ATOM 2 CA SER A 1 16.318 13.369 2.512 1.00 54.83
C
<<<<script compiler ERROR: unexpected end of script command
----
load DATA >>>> "mydata
ATOM 1 N SER A 1 15.489 14.526 2.933 1.00 57.01
N
ATOM 2 CA SER A 1 16.318 13.369 2.512 1.00 54.83
C
ATOM 3 C SER A 1 15.426 12.149 2.340 1.00 52.04
C
<<<<script compiler ERROR: unexpected end of script command
----
load DATA >>>> "mydata
ATOM 1 N SER A 1 15.489 14.526 2.933 1.00 57.01
N
ATOM 2 CA SER A 1 16.318 13.369 2.512 1.00 54.83
C
ATOM 3 C SER A 1 15.426 12.149 2.340 1.00 52.04
C
ATOM 4 O SER A 1 14.566 11.882 3.181 1.00 54.25
O
<<<<script compiler ERROR: unexpected end of script command
----
.
.
.
-------------------------------------------------------------
It is just the beginning. It looks as if Jmol would like to print a new
error message for each input line, including all former lines into each
error message.
Maybe related to the high memory consumption is another memory-related
observation I made recently:
In the application the there are shown two numbers about the memory used
by Jmol at the bottom right. The amount of memory used increases about
20-30 megabytes for each command I enter into the script console,
seemingly independent of the command itself.
Regards,
Rolf
--
Rolf Huehne
Postdoc
Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany
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