[Gate-users] Transfering Files to Shared Folder

[Martin Purschke]

Hi Lars,

long time no see!

I'm mostly a bystander when it comes to running Gate (which we use a lot
in our medical imaging group), but this looks in part like the well-kown
windows vs linux text file issue, and in part like a permission/file
access issue.

A macro (text) file has its lines delimited by a linefeed ( character
10) on Linux, but under Windows, the delimiter is a carriage-return
(char 13) followed by a linefeed (10). Often, although far from always,
linux understands either; this depends on whether or not a standard
input-parsing library such as "readline" is being used, or some
home-grown code is at work.

There are system utilities unix2dos and dos2unix on linux which do the
conversion for you.

Please use a set of local files in a test to see if this is the issue
with *reading* them.

The files being shown in red with question marks is a different matter
entirely. This points to some issue with cross-mounting the file
systems, and is hard to debug by email. Let me just say how I approach
this when I need to cater to the windows-using crowd:

The Linux machines all send their files to a NFS-mounted disk on a
central server. You want one, or at most a very small number, of such
filesystems. That's all that the linux nodes really need to know. They
never leave their universe, so to speak.

That server, in addition to NFS-exporting said file system, also exports
it as a samba/cifs share, so to Windows machines it looks just like any
other disk shared by an actual Windows box. Your Win desktop mounts that
share, and all the files are at your fingertips. It also gives you
extremely fine-grained access control for the directories and files if
that's what you need. On standard Linux distros, have a look at the
/etc/samba/smb.conf file, but get expert help if you're unsure what you
are exporting here.

Virtually all Linux distros have the ability to do that, although samba
may not be installed. Remember that only the actual file server needs to
have this ability, not all the cluster nodes individually.

Hope it helps. Also good to hear from you again.

Best,
	Martin



On 7/9/14, 6:13 PM, LARS.EWELL at HAMPTONU.EDU wrote:
> To Whom it May Concern,
> 
>  
> 
>   I have been transferring files from our linux cluster to my local
> desktop, on which I’m running a copy of vGATE.
> 
>  
> 
>   Per the instructions in the Oracle Virtual Box manual, I  mount the
> Windows folder onto a directory in the virtual machine running Ubutnu
> linux, and I can transfer the files.
> 
>  
> 
>   The problem arises when I look over the files in Ubutnu.  Sometimes
> the files, which are GATE ‘.mac’ text files, appear in red text when
> looking at them in Ubutnu linux.  The system does not recognize them and
> if I do an ‘ls –l’, I get a series of question marks where the
> read-write information would normally be.  I thought it was due to the
> file extension (mac), but that turned out not to be the case.
> 
>  
> 
>   It seems random and I have a hard time getting Ubutnu linux to
> recognize the .mac files I have been transferring from my Windows
> machine to the virtual machine running Ubutnu via a sharred folder.
> 
>  
> 
>   Any suggestions?  I have played with ascii and binary transfer with my
> copy of WinSCP I’m using to transfer the files from our linux cluster to
> my Windows machine.
> 
>  
> 
>   Thanks in advance.
> 
>  
> 
>   Regards,
> 
>  
> 
>   Lars Ewell
> 
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-- 
Martin L. Purschke, Ph.D.        ;   purschke at bnl.gov
                                 ;   http://www.phenix.bnl.gov/~purschke
                                 ;
Brookhaven National Laboratory   ;   phone: +1-631-344-5244
Physics Department Bldg 510 C    ;   fax:   +1-631-344-3253
Upton, NY 11973-5000             ;   skype: mpurschke
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