Re: [HCP-Users] [Mac OSX] ERROR from cp --preserve=timestamps when running FreeSurferHiresWhite

2017-05-17 Thread Sang-Young Kim 
Dear Tim:

Thank you so much for your help. I will use cp -p instead of using cp 
-preserve==timestamps. 

Sang-Young


> On May 17, 2017, at 1:13 PM, Timothy B. Brown  wrote:
> 
> Dear Sang-Young,
> 
> I would suggest that you replace the cp --preserve=timestamps commands in the 
> scripts that are causing the problems with cp -p commands.
> 
> Until March 2016, those scripts used cp -p with the specific intent of 
> preserving timestamps on the files that were copied. In the environment we 
> currently use to run pipelines here at Washington University in St. Louis, 
> the cp -p command was failing. The cp -p command is equivalent to cp 
> --preserve=mode,ownership,timestamps. In our environment, it was not possible 
> to preserve the ownership of files when doing those copies. Thus the cp -p 
> command was failing.
> Since the actual intent of the command was only to preserve the timestamps 
> and preserving the other items (mode and ownership) was not particularly 
> important, the commands were changed to cp --preserve=timestamps (asking only 
> to preserve what is necessary). 
> We have since learned that for at least some versions of Mac OSX, the 
> --preserve= option is not supported for the cp command. However, the -p 
> option seems to still be supported in Mac OSX. 
> The situation now is that changing the command back to cp -p will not work 
> for us, and leaving it as cp --preserve=timestamps will not work for people 
> using some versions of Mac OSX.
> 
> It is my understanding that using Gnu CoreUtils on Mac OSX makes the 
> --preserve= option to the cp command available under Mac OSX. But I have no 
> experience with that, so I'm not in a position to recommend it.
> 
> I'm sorry for your frustration in dealing with this issue. Thank you for 
> asking this on the list. Hopefully, this reply will prevent some others from 
> experiencing the same frustration.
>  
>   Tim
> 
> On 05/17/2017 09:31 AM, Sang-Young Kim wrote:
>> Dear HCP users:
>> 
>> In FreeSureferPipeline script (e.g., FreeSurferHiresWhite), it looks like 
>> that cp --preserve=timestamps option does not work in Mac OSX. 
>> I have spent lots of times to fix this problem and cause a lot of 
>> frustration. 
>> 
>> My question is that whether I can use the option rsync -t to copy lh.white, 
>> lh.curv etc.. as an alternative method?
>> I’m not sure rsync -t can also be used to preserve the timestamps on the 
>> files copied. 
>> Are there any other method to fix this problem?
>> 
>> It’ll be greatly appreciated if you can give me any solution. 
>> 
>> Thanks in advance. 
>> 
>> Sang-Young
>> 
>> 
>> 
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org 
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
>> 
> 
> -- 
> Timothy B. Brown
> Business & Technology Application Analyst III
> Pipeline Developer (Human Connectome Project)
> tbbrown(at)wustl.edu
> The material in this message is private and may contain Protected Healthcare 
> Information (PHI). If you are not the intended recipient, be advised that any 
> unauthorized use, disclosure, copying or the taking of any action in reliance 
> on the contents of this information is strictly prohibited. If you have 
> received this email in error, please immediately notify the sender via 
> telephone or return mail.


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Re: [HCP-Users] [Mac OSX] ERROR from cp --preserve=timestamps when running FreeSurferHiresWhite

2017-05-17 Thread Timothy B. Brown 

Dear Sang-Young,

I would suggest that you replace the cp --preserve=timestamps commands 
in the scripts that are causing the problems with cp -p commands.


Until March 2016, those scripts used cp -p with the specific intent of 
preserving timestamps on the files that were copied. In the environment 
we currently use to run pipelines here at Washington University in St. 
Louis, the cp -p command was failing. The cp -p command is equivalent to 
cp --preserve=mode,ownership,timestamps. In our environment, it was not 
possible to preserve the ownership of files when doing those copies. 
Thus the cp -p command was failing.


Since the actual intent of the command was only to preserve the 
timestamps and preserving the other items (mode and ownership) was not 
particularly important, the commands were changed to cp 
--preserve=timestamps (asking only to preserve what is necessary).


We have since learned that for at least some versions of Mac OSX, the 
--preserve= option is not supported for the cp command. However, the -p 
option seems to still be supported in Mac OSX.


The situation now is that changing the command back to cp -p will not 
work for us, and leaving it as cp --preserve=timestamps will not work 
for people using some versions of Mac OSX.


It is my understanding that using Gnu CoreUtils on Mac OSX makes the 
--preserve= option to the cp command available under Mac OSX. But I have 
no experience with that, so I'm not in a position to recommend it.


I'm sorry for your frustration in dealing with this issue. Thank you for 
asking this on the list. Hopefully, this reply will prevent some others 
from experiencing the same frustration.


  Tim

On 05/17/2017 09:31 AM, Sang-Young Kim wrote:

Dear HCP users:

In FreeSureferPipeline script (e.g., FreeSurferHiresWhite), it looks like that 
cp --preserve=timestamps option does not work in Mac OSX.
I have spent lots of times to fix this problem and cause a lot of frustration.

My question is that whether I can use the option rsync -t to copy lh.white, 
lh.curv etc.. as an alternative method?
I’m not sure rsync -t can also be used to preserve the timestamps on the files 
copied.
Are there any other method to fix this problem?

It’ll be greatly appreciated if you can give me any solution.

Thanks in advance.

Sang-Young



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--
/Timothy B. Brown
Business & Technology Application Analyst III
Pipeline Developer (Human Connectome Project)
tbbrown(at)wustl.edu
/

The material in this message is private and may contain Protected 
Healthcare Information (PHI). If you are not the intended recipient, be 
advised that any unauthorized use, disclosure, copying or the taking of 
any action in reliance on the contents of this information is strictly 
prohibited. If you have received this email in error, please immediately 
notify the sender via telephone or return mail.


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