Dear Jason,
It still doesn't work after adding "-nomtkpp" flag. And I
decide to give the installation in Cygwin up.
Thank you for your
2012/7/19 Jason Swails <jason.swails.gmail.com>
> When you run configure, use the "-nomtkpp" flag. MTK++ has had plenty of
> issues in the past with Cygwin. If you don't need MTK++, then this does
> not matter. If you do, perhaps Dan can provide advice about getting it
> working on Win7 if he was able to, but a better idea would be to get ahold
> of some kind of Unix system somehow.
>
> HTH,
> Jason
>
> On Thu, Jul 19, 2012 at 3:36 AM, 钟舜 <zhongshun0643.gmail.com> wrote:
>
>> Dear Jason,
>> It is some patches of "netcdf" "hdf5" and "_autorebase". But
>> I'm sorry to forget the exact name of these small patches. I didn't
>> remember to write their name down when reinstallation.
>> But I still get a warning after I typed "make install" and the
>> installation failed at last.
>>
>> 警告： (1)处的 DO 循环会被执行零次
>> netcdf_text_variables.f90:60.93:
>> 包含于 netcdf.f90:51：
>> numDims ) = (/ 1, (product(localCount(:counter)), counter = 1, numDims -
>> 1) /)
>>
>> 1
>> 警告： (1)处的 DO 循环会被执行零次
>> /bin/sh ../libtool --mode=link gfortran -I../libsrc -I. -O3 -o
>> libnetcdff90.la typeSizes.lo netcdf.lo
>> See any operating system documentation about shared libraries for
>> more information, such as the ld(1) and ld.so(8) manual pages.
>> ----------------------------------------------------------------------
>> test -z "/home/administrator/amber12/lib/pkgconfig" || /usr/bin/mkdir -p
>> "/home/administrator/amber12/lib/pkgconfig"
>> /usr/bin/install -c -m 644 fftw3.pc
>> '/home/administrator/amber12/lib/pkgconfig'
>> make[4]: 离开目录“/home/administrator/amber12/AmberTools/src/fftw-3.3”
>> make[3]: 离开目录“/home/administrator/amber12/AmberTools/src/fftw-3.3”
>> Making install in tests
>> make[3]: 进入目录“/home/administrator/amber12/AmberTools/src/fftw-3.3/tests”
>> make[4]: 进入目录“/home/administrator/amber12/AmberTools/src/fftw-3.3/tests”
>> make[4]: 对“install-exec-am”无需做任何事。
>> make[4]: 对“install-data-am”无需做任何事。
>>
>> ~
>> ~
>> ~
>> ~
>>
>> Starting installation of MTK++ at 2012年07月19日 15:20:52.
>> (cd mtkpp && make && make -j 1 install )
>> make[2]: 进入目录“/home/administrator/amber12/AmberTools/src/mtkpp”
>> make[2]: *** 没有指明目标并且找不到 makefile。 停止。
>> make[2]: 离开目录“/home/administrator/amber12/AmberTools/src/mtkpp”
>> Makefile:106: recipe for target `install_mtkpp' failed
>> make[1]: *** [install_mtkpp] Error 2
>> make[1]: 离开目录“/home/administrator/amber12/AmberTools/src”
>> Makefile:7: recipe for target `install' failed
>> make: *** [install] Error 2
>>
>> I really don't know what should I do now.
>>
>> Shun Zhong
>>
>> 2012/7/19 Jason Swails
>>>
>>> <jason.swails.gmail.com>
>>
>>
>>
>>> This is OK. I think this has to do with line endings (DOS and Unix do
>>> theirs differently). IMO, you can safely ignore this failure. Just re-run
>>> patch_amber.py with the --ignore-fails flag. i.e.:
>>>
>>>
>>> cd $AMBERHOME
>>> ./patch_amber.py --update-tree --ignore-fails
>>>
>>>
>>> Then you should be good to run configure and build Amber.
>>>
>>>
>>> Out of curiosity, which packages had you forgotten?
>>>
>>>
>>> All the best,
>>> Jason
>>>
>>> On Wed, Jul 18, 2012 at 10:38 PM, 钟舜 <zhongshun0643.gmail.com> wrote:
>>>
>>>
>>>> Dear jason，
>>>>
>>>> First， I feel very upset for my OS is Win7.
>>>> But I still try to check the Cygwin setup back up as you
>>>> advise. There are indeed two little items remained "skip". After
>>>> reinstallation of the Cygwin, the error is gone.
>>>> I have learnt the lesson again: "Be careful whatever you
>>>> do."
>>>> But unfortunately I encounter a new error:
>>>> Applying AmberTools12 patches
>>>> Error or warning during patching process for
>>>> .patches/AmberTools_Unapplied_Patches/bugfix.4:
>>>> 4 out of 4 hunks FAILED -- saving rejects to file
>>>> AmberTools/test/mmpbsa_py/08_Stability/FINAL_DECOMP_MMPBSA2.csv.save.rej
>>>> I am approaching breakdown, maybe I should give up now.
>>>>
>>>> Shun Zhong
>>>>
>>>> 2012/7/19 Jason Swails <jason.swails.gmail.com>
>>>>
>>>>
>>>>> You should keep these replies on the Amber mailing list so others stay
>>>>> generally informed and so you can benefit from others' experiences and
>>>>> advice.
>>>>>
>>>>>
>>>>> Your error suggests something has gone awry with the mechanism that
>>>>> the patch_amber.py Python script uses to try to access the web. I'm
>>>>> not sure why the first message is coming about (the one about address
>>>>> space) -- I don't know if it's a memory issue (seems unlikely), or if some
>>>>> later version of Windows has broken this part of Cygwin.
>>>>>
>>>>>
>>>>> I don't think it's possible for me (or anybody else, most likely) to
>>>>> help fix this behavior unless we can reproduce the issue. So please follow
>>>>> these steps:
>>>>>
>>>>>
>>>>> Open the Cygwin setup back up and go through carefully to make sure
>>>>> that every package listed on
>>>>> http://jswails.wikidot.com/windows-cygwin is selected and installed.
>>>>> If it is, and you are still getting these errors, then respond back (to
>>>>> the list) with the OS you are using (is it Windows 7, XP, Vista, ...?)
>>>>>
>>>>>
>>>>> I've only tested the Cygwin install on Windows XP, and it's worked
>>>>> fine for me. It's always possible that Windows 7 (or some upgrade therein)
>>>>> has broken Cygwin's urllib module in its Python.
>>>>>
>>>>>
>>>>> You can always download the patches one-by-one and apply them using
>>>>> "./patch_amber.py --apply <patch_file>" (it never attempts to go online to
>>>>> find it at that point).
>>>>>
>>>>>
>>>>> You can also set up a guest Linux OS in a virtual machine (google for
>>>>> VirtualBox) and operate with Amber in there (this is probably the easiest
>>>>> route, since Linux/Mac are the best-tested platforms by the developers).
>>>>>
>>>>>
>>>>> HTH,
>>>>> Jason
>>>>>
>>>>> On Wed, Jul 18, 2012 at 2:15 AM, 钟舜 <zhongshun0643.gmail.com> wrote:
>>>>>
>>>>>
>>>>>> Dear jason，
>>>>>>
>>>>>> Thank for your answer and it's very helpful. But I
>>>>>> receive a new error after reinstallation of cygwin as you advised. The
>>>>>> error is as follows:
>>>>>>
>>>>>>
>>>>>> Applying AmberTools12 patches
>>>>>> 1 [main] python2.6 8624 child_info_fork::abort: address space
>>>>>> needed by 'fcntl.dll' (0x3D0000) is already occupied
>>>>>> Traceback (most recent call last):
>>>>>> File "./patch_amber.py", line 958, in <module>
>>>>>> if ipatch.apply_patch() and not opt.ignore_fails: sys.exit(1)
>>>>>> File "./patch_amber.py", line 271, in apply_patch
>>>>>> process = Popen(args, stdin=patch_file, stdout=PIPE, stderr=PIPE)
>>>>>> File "/usr/lib/python2.6/subprocess.py", line 623, in __init__
>>>>>> errread, errwrite)
>>>>>> File "/usr/lib/python2.6/subprocess.py", line 1051, in
>>>>>> _execute_child
>>>>>> self.pid = os.fork()
>>>>>> OSError: [Errno 11] Resource temporarily unavailable
>>>>>> Automatic patching failed! Check the errors before re-configuring
>>>>>>
>>>>>>
>>>>>> I have tried many times, but it still gives this error. I don't know
>>>>>> how long the "temporarily" means, or I must do something to solve this
>>>>>> error.
>>>>>>
>>>>>> Best regards!
>>>>>> Shun Zhong
>>>>>>
>>>>>> ---------------
>>>>>> shun zhong
>>>>>> Graduate Student of Technical Institute of Physcis and Chemistry, CAS
>>>>>> Beijing, P.R.China, 100190
>>>>>> Web: htthttp://www.ipc.ac.cn/
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Jason M. Swails
>>>>> Quantum Theory Project,
>>>>> University of Florida
>>>>> Ph.D. Candidate
>>>>> 352-392-4032
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> Jason M. Swails
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Candidate
>>> 352-392-4032
>>>
>>>
>>
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
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Received on Thu Jul 19 2012 - 18:00:03 PDT
