R help - Aug 2012 - Error: ReadItem: unknown type 98, perhaps written by later version of R

Hi,

I am running a large number of jobs (thousands) in parallel (linux OS 
64bit), R version 2.14.1 (2011-12-22), Platform: x86_64-redhat-linux-gnu 
(64-bit). Up to yesterday everything ran fine with jobs in several 
blocks (block1, block2 etc) of submission. They are sent to an LSF 
platform to handle the parallel submission. Today I see that only one of 
the blocks (the 19) has not finished correct:
It reports in the out file:

Error: ReadItem: unknown type 98, perhaps written by later version of R
Execution halted

Checking through google one had recommended rm ~/.RData
I applied it, but the run again fails, when submitting through SAS for 
block 19.

[SAS in macro lang.] %sysexec bsub R CMD BATCH &fullpath./dc19at&j..R 
&fullpath.dc19at&j..out ;
[SAS ] %sysexec sleep 3 ;
   <looping through jobs in a block>

If I go to the directory where the R program and the data reside and 
apply the same command by hand

R CMD BATCH dc19at1.R dc19at1.out
it works with no problem.

But if I use a similar program (SAS program)

that has been executing the same command successfully for thousand of 
jobs in other blocks, the jobs for the block 19 fail.

Error: ReadItem: unknown type 98, perhaps written by later version of R
Execution halted

even in the one I just mentioned if I execute by hand goes well.

Do you know what could be the cause of bsub submission to fail? Any remedy?

Thank you in advance,

Aldi

--

Hi,

Here is a solution for this type of error:
Error: ReadItem: unknown type 98, perhaps written by later version of R
Execution halted

Created a script file under the directory where the pgm-s and data 
reside and ran there

./script.sh

where script.sh had the following lines
R CMD BATCH ./dc19at1.R ./dc19at1.out
sleep 3
R CMD BATCH ./dc19at2.R ./dc19at2.out
sleep 3
...
etc

The programs ran with no problem.

So what I did is eliminated the full path let's say
R CMD BATCH /a/b/c/dc19at1.R /a/b/c/dc19at1.out
which did not work through bsub or at the command line in a remote server.

I am not sure what is the "type 98 error" meaning in R?
Anybody knows where the R error types are described?

TIA,

Aldi

On 8/21/2012 10:09 AM, Aldi Kraja wrote:
> Hi,
>
> I am running a large number of jobs (thousands) in parallel (linux OS 
> 64bit), R version 2.14.1 (2011-12-22), Platform: 
> x86_64-redhat-linux-gnu (64-bit). Up to yesterday everything ran fine 
> with jobs in several blocks (block1, block2 etc) of submission. They 
> are sent to an LSF platform to handle the parallel submission. Today I 
> see that only one of the blocks (the 19) has not finished correct:
> It reports in the out file:
>
> Error: ReadItem: unknown type 98, perhaps written by later version of R
> Execution halted
>
> Checking through google one had recommended rm ~/.RData
> I applied it, but the run again fails, when submitting through SAS for 
> block 19.
>
> [SAS in macro lang.] %sysexec bsub R CMD BATCH
&fullpath./dc19at&j..R
> &fullpath.dc19at&j..out ;
> [SAS ] %sysexec sleep 3 ;
>   <looping through jobs in a block>
>
> If I go to the directory where the R program and the data reside and 
> apply the same command by hand
>
> R CMD BATCH dc19at1.R dc19at1.out
> it works with no problem.
>
> But if I use a similar program (SAS program)
>
> that has been executing the same command successfully for thousand of 
> jobs in other blocks, the jobs for the block 19 fail.
>
> Error: ReadItem: unknown type 98, perhaps written by later version of R
> Execution halted
>
> even in the one I just mentioned if I execute by hand goes well.
>
> Do you know what could be the cause of bsub submission to fail? Any 
> remedy?
>
> Thank you in advance,
>
> Aldi
>
> -- 
>
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