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Re: [Stochkit-mailinglist] sh: Syntax error: Bad fd number

[Sheng Wu <sh...@um...>]

Hi Wen-Shyong,
This is probably because your shell does not support the redirecting  
command ">&". There are two ways to solve that:
1.
go to src/drivers/ParallelIntervalSimulation.cpp  line 95
change
" >&  
"+commandLine.getOutputDir()+"/.StochKit/thread-log"+threadNumString+".txt"
to
"  
 >"+commandLine.getOutputDir()+"/.StochKit/thread-log"+threadNumString+".txt  
2>&1"
then go to src/utility/StandardDriverUtilities.cpp line 114
change
" >& "+currentPath+"/"+commandLine.getGeneratedCodeDir()+"/.compile-log.txt"
to
"  
 >"+currentPath+"/"+commandLine.getGeneratedCodeDir()+"/.compile-log.txt  
2>&1"

2. If 1 doesn't work, try to change your default sh to bash:
sudo rm /bin/sh
sudo ln -s /bin/bash /bin/sh

Let me know if that solves your problem.
Best,
Sheng

Quoting Wen-Shyong Tzou <ws...@nt...>:

> Dear Lady and Sir,
>
>     I run ./ssa in Ubuntu and encountered an error "sh: Syntax  
> error: Bad fd number". Any suggestion is welcomed.
>
> #####################################
>
>     wstzou@paris:~/StochKit2beta.1$ ./ssa -m  
> models/examples/heat_shock.xml -t 10 -r 1000
> StochKit MESSAGE: determining appropriate driver...running  
> $STOCHKIT_HOME/bin/ssa_odm_mixed_small...
> StochKit MESSAGE: compiling generated code...this will take a few moments...
> sh: Syntax error: Bad fd number
> StochKit ERROR: compile of generated code failed.  Simulation terminated.
> cp: cannot stat  
> `/home/wstzou/StochKit2beta.1/models/examples/heat_shock_generated_code/.compile-log.txt': No such file or  
> directory
> Check log file  
> "models/examples/heat_shock_generated_code/compile-log.txt" for  
> error messages.
> ######################################
>
> Thanks a lot in advance,
>
> ------------------------------------------------------
> ???
> 202 ?????????2?
> ?????????????
>
> Wen-Shyong Tzou
> Assistant Professor
> Institute of Bioscience and Biotechnology
> National Taiwan Ocean University
> 2, Pei-Ning Road, Keelung, Taiwan 20224, R. O. C.
> Office: 886-2-2462 2192 ext 5522
> Fax: 886-2-2462 2320
> Cellular: 0928 305 905
> E-mail: ws...@nt...
> http://biofun.imbt.ntou.edu.tw/web/index.htm

[Stochkit-mailinglist] sh: Syntax error: Bad fd number

[Wen-Shyong T. <ws...@nt...>]

Dear Lady and Sir,

    I run ./ssa in Ubuntu and encountered an error "sh: Syntax error: Bad fd number". Any suggestion is welcomed.

#####################################

    wstzou@paris:~/StochKit2beta.1$ ./ssa -m models/examples/heat_shock.xml -t 10 -r 1000
StochKit MESSAGE: determining appropriate driver...running $STOCHKIT_HOME/bin/ssa_odm_mixed_small...
StochKit MESSAGE: compiling generated code...this will take a few moments...
sh: Syntax error: Bad fd number
StochKit ERROR: compile of generated code failed.  Simulation terminated.
cp: cannot stat `/home/wstzou/StochKit2beta.1/models/examples/heat_shock_generated_code/.compile-log.txt': No such file or directory
Check log file "models/examples/heat_shock_generated_code/compile-log.txt" for error messages.
######################################

Thanks a lot in advance,

------------------------------------------------------
鄒文雄
202 基隆市中正區北寧路2號
台灣海洋大學生物科技研究所
 
Wen-Shyong Tzou
Assistant Professor
Institute of Bioscience and Biotechnology
National Taiwan Ocean University
2, Pei-Ning Road, Keelung, Taiwan 20224, R. O. C.
Office: 886-2-2462 2192 ext 5522
Fax: 886-2-2462 2320
Cellular: 0928 305 905
E-mail: ws...@nt...
http://biofun.imbt.ntou.edu.tw/web/index.htm