[Mono-dev] Compilation help / error CS2001

[Rafael Teixeira]

Inline,

Rafael Teixeira
O..:.)oooo

On Wed, May 31, 2017 at 7:51 PM, Chandler <admin at genome.arizona.edu> wrote:

> Thank you Rafael, yes very helpful.  I made a script "compade" like you
> suggested and put it in the path.  We are able to run conpade now but there
> are some minor issues left.
>
> It seems the program can only be run when the cwd is where ConPADE.exe is,
> because otherwise it can't find other required files.  For example, when i
> try to run it from my home dir, it can't find /opt/MicrosoftGenomics/ConPADE/errorModel.bin
> (see below).
>

The conpade program would better search for the error model in the app
location, not in the current directory. You can change the wrapper script
adding a  'cd /opt/MicrosoftGenomics/ConPADE'  line before calling mono but
then you would need to always pass the full path to your ,BAM file, as
you've done in your example below.


>
> Another question i have, is there a way to have mono use multiple
> threads?  Or is that something the .exe file needs to be compiled with?
> When i run it, "mono" only uses 1 thread so it would be nice to get it
> going faster.  From what i could find, i tried modifying the script so it
> has "mono --aot threads=10" for example but this returns an error:
> "Cannot open assembly 'threads=10': No such file or directory."
>
> AFAIR, There is no syntax to tell Mono how many threads to use, it uses as
many as the OS allow, but only if the program asks for it.

Mono uses at least two threads in each process, but the program must be
explicitly coded to use more threads if it desires, but I don't think the
kind of calculations this program does can be made in parallel, so it
possibly just can't use more threads, to speed things

It seems that you are mixing concepts, mono is a runtime and enables lots
of capabilities for the programs you run with it, like multiple threads,
but the program itself exercises those capabilities or not, depending on
what the programmer intended or the constrains of the problem he developed
the program to try to solve.

If I were you, I would ask the maintainers for the program and the Bio
libraries if they can address these two concerns: how to correctly find the
location of the errorModel.bin file, and if the calculations can be
parallelized and thus benefit from multiple threads.



> Thanks
>
>
> ~]$ conpade -bamName /opt/MicrosoftGenomics/ConPADE/TestData.bam
>
> Unhandled Exception:
> System.Exception: Run failure. ---> System.IO.FileNotFoundException: File
> errorModel.bin not found.
>   at ConPADE.ConPADE.Error_Probs () [0x00049] in
> <4e54a4850a3c4c209a91638afe30e0c4>:0
>   at ConPADE.ConPADE.RunFile (System.String bamName) [0x00051] in
> <4e54a4850a3c4c209a91638afe30e0c4>:0
>   at ConPADE.ConPADE.RunTasks (Bio.Util.RangeCollection tasksToRun,
> System.Int64 taskCount) [0x0000c] in <4e54a4850a3c4c209a91638afe30e0c4>:0
>   at Bio.Util.Distribute.Locally.Distribute (Bio.Util.Distribute.IDistributable
> distributableObject) [0x0003c] in <992c28500da945aba2070d505f06da7d>:0
>   at Bio.Util.Distribute.SelfDistributable.Run () [0x0000e] in
> <992c28500da945aba2070d505f06da7d>:0
>   at Bio.Util.ArgumentParser.ArgumentCollection.ConstructAndRun[T] ()
> [0x00009] in <992c28500da945aba2070d505f06da7d>:0
>    --- End of inner exception stack trace ---
>   at Bio.Util.ArgumentParser.ArgumentCollection.ConstructAndRun[T] ()
> [0x00058] in <992c28500da945aba2070d505f06da7d>:0
>   at Bio.Util.ArgumentParser.CommandArguments.ConstructAndRun[T]
> (System.String[] commandArgs, System.Boolean generateHelpPage) [0x0000e] in
> <992c28500da945aba2070d505f06da7d>:0
>   at Bio.Util.ArgumentParser.CommandArguments.ConstructAndRun[T]
> (System.String[] commandArgs) [0x00000] in <992c28500da945aba2070d505f06d
> a7d>:0
>   at ConPADE.ConPADE.Main (System.String[] args) [0x00000] in
> <4e54a4850a3c4c209a91638afe30e0c4>:0
> [ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: Run failure. --->
> System.IO.FileNotFoundException: File errorModel.bin not found.
>   at ConPADE.ConPADE.Error_Probs () [0x00049] in
> <4e54a4850a3c4c209a91638afe30e0c4>:0
>   at ConPADE.ConPADE.RunFile (System.String bamName) [0x00051] in
> <4e54a4850a3c4c209a91638afe30e0c4>:0
>   at ConPADE.ConPADE.RunTasks (Bio.Util.RangeCollection tasksToRun,
> System.Int64 taskCount) [0x0000c] in <4e54a4850a3c4c209a91638afe30e0c4>:0
>   at Bio.Util.Distribute.Locally.Distribute (Bio.Util.Distribute.IDistributable
> distributableObject) [0x0003c] in <992c28500da945aba2070d505f06da7d>:0
>   at Bio.Util.Distribute.SelfDistributable.Run () [0x0000e] in
> <992c28500da945aba2070d505f06da7d>:0
>   at Bio.Util.ArgumentParser.ArgumentCollection.ConstructAndRun[T] ()
> [0x00009] in <992c28500da945aba2070d505f06da7d>:0
>    --- End of inner exception stack trace ---
>   at Bio.Util.ArgumentParser.ArgumentCollection.ConstructAndRun[T] ()
> [0x00058] in <992c28500da945aba2070d505f06da7d>:0
>   at Bio.Util.ArgumentParser.CommandArguments.ConstructAndRun[T]
> (System.String[] commandArgs, System.Boolean generateHelpPage) [0x0000e] in
> <992c28500da945aba2070d505f06da7d>:0
>   at Bio.Util.ArgumentParser.CommandArguments.ConstructAndRun[T]
> (System.String[] commandArgs) [0x00000] in <992c28500da945aba2070d505f06d
> a7d>:0
>   at ConPADE.ConPADE.Main (System.String[] args) [0x00000] in
> <4e54a4850a3c4c209a91638afe30e0c4>:0
>
> ~]$
>
>
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