Re: amber-developers: Re: PMEMD 10 patch 2

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Fri, 3 Oct 2008 13:29:33 -0400

On Fri, Oct 3, 2008 at 1:03 PM, Robert Duke wrote:
> Well, I guess my comments are directed at lowering expectations for perfect
> compatibility; you may get your cygwin stuff to work 99.9% of the time, but
> I've played this game at the system interface level, and not everything will
> work.

Well, personally I have not find many problems to date, and I believe
the Cygwin developers deserve some good praise for it. Cygwin has
worked wonderfully for me for a good time. Of course, I'm no "power
user", and only do basic things in cygwin, real calculations are
reserved for real (Linux/Unix) machines.

Most problems I've heard about from other users generally come from
the use of DOS style line endings when cygwin expects UNIX style, and
those can be solved with 'dos2unix' pretty easily.

> Are there possibly differences in the filesystems you guys are
> running on top of here? I would expect NTFS to do a better job than FAT or
> FAT32, though I have not kept up with where NTFS is at in being able to
> emulate a unix filesystem.

Myself, I use NTFS, as do most Windows XP users, so I just assumed
it's the same for Dave. Instead, I would look for some not default
shell options that may be turned on there.

> I would probably dual boot my laptop rather than
> using something like cygwin myself, but that has a lot to do with being
> driven crazy by subtle incompatibilities.

LOL, I guess I've been lucky so far... :-)

Regards,
Gustavo.


> Regards - Bob
> ----- Original Message ----- From: "David A. Case"
> <case.biomaps.rutgers.edu>
> To: <amber-developers.scripps.edu>
> Sent: Friday, October 03, 2008 12:11 PM
> Subject: Re: amber-developers: Re: PMEMD 10 patch 2
>
>
>> On Fri, Oct 03, 2008, Gustavo Seabra wrote:
>>>
>>> Weird... it works just fine for me. What's your 'diff' version? I'm
>>> using Cygwin 1.5.25-15, and:
>>>
>>> $ diff -v
>>> diff (GNU diffutils) 2.8.7
>>>
>>> $ patch -v
>>> patch 2.5.8
>>
>> I have the same versions. And (in spite of Bob's comments) it is quite
>> unusual for something like this to fail on cygwin. So there may be
>> something
>> about my setup that is inconsistent.
>>
>> Here is my test, looks like yours(?):
>>
>> gibbs% echo "abcdef" > test_file
>> gibbs% diff -Naur /dev/null test_file > patch1
>> gibbs% cat patch1
>> --- /dev/null 2006-11-30 19:00:00.000000000 -0500
>> +++ test_file 2008-10-03 11:48:59.281250000 -0400
>> .@ -0,0 +1 @@
>> +abcdef
>> gibbs% rm test_file
>> rm: remove regular file `test_file'? y
>> gibbs% patch -N < patch1
>> can't find file to patch at input line 3
>> Perhaps you should have used the -p or --strip option?
>> The text leading up to this was:
>> --------------------------
>> |--- /dev/null 2006-11-30 19:00:00.000000000 -0500
>> |+++ test_file 2008-10-03 11:48:59.281250000 -0400
>> --------------------------
>> File to patch:
>>
>>
>>
>> If I do a "touch test_file" right before patch, so that it is a
>> zero-length
>> file, then the patch command works. So, the "can't find file to patch"
>> statement is indeed referring to "test_file" and not to "/dev/null".
>>
>> Note also: if test_file does not exist, and I type "patch testfile <
>> patch1",
>> things work.
>>
>> This may all be clear once I figure it out, but right now it is not so
>> clear.
>>
>> ...thx..dac
Received on Sun Oct 05 2008 - 05:07:58 PDT
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