Dear AMBER Users,
I would like to test AMBER18 with GPUs but the code seems to fail when
applying the updates.
After downloading and extracting the source code, I attempted to compile it
by
./configure gpu
The updating seems to be fine until it runs into update.10 (AmberTools).
The error message is marked in bold and italic.
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 18 patches:
update.1, update.2, update.3, update.4, update.5, update.6, update.7,
update.8, update.9, update.10,
update.11
Available Amber 18 patches:
update.1 (modifies pmemd)
update.2 (modifies pmemd)
update.3 (modifies pmemd)
update.4 (modifies pmemd.cuda)
update.5 (modifies pmemd)
update.6 (modifies pmemd.cuda)
update.7 (modifies pmemd.cuda)
update.8 (modifies pmemd)
update.9 (modifies pmemd.cuda)
There are patches available. Do you want to apply them now? [y/N]
(Recommended Y)
y
Preparing to apply updates... please wait.
Downloading updates for AmberTools 18
Downloading AmberTools 18/update.1 (6.03 KB)
Applying AmberTools 18/update.1
Downloading AmberTools 18/update.2 (2.98 KB)
Applying AmberTools 18/update.2
Downloading AmberTools 18/update.3 (8.19 KB)
Applying AmberTools 18/update.3
Downloading AmberTools 18/update.4 (1.09 KB)
Applying AmberTools 18/update.4
Downloading AmberTools 18/update.5 (1.37 KB)
Applying AmberTools 18/update.5
Downloading AmberTools 18/update.6 (43.31 KB)
Applying AmberTools 18/update.6
Downloading AmberTools 18/update.7 (944 Bytes)
Applying AmberTools 18/update.7
Downloading AmberTools 18/update.8 (30.37 KB)
Applying AmberTools 18/update.8
Downloading AmberTools 18/update.9 (2.90 KB)
Applying AmberTools 18/update.9
Downloading AmberTools 18/update.10 (1108.29 KB)
*Downloading: [:::::::::::::::::::::::::::::::::::::: ]
76.9%Traceback (most recent call last):*
* File "./update_amber", line 26, in <module>*
* app.mainloop()*
* File "/home/ruisun.hawaii/amber/amber18-gpu/updateutils/main.py", line
526, in mainloop*
* self.update()*
* File "/home/ruisun.hawaii/amber/amber18-gpu/updateutils/main.py", line
49, in newfcn*
* fcn(self, *args, **kwargs)*
* File "/home/ruisun.hawaii/amber/amber18-gpu/updateutils/main.py", line
348, in update*
* self._update_ambertools()*
* File "/home/ruisun.hawaii/amber/amber18-gpu/updateutils/main.py", line
49, in newfcn*
* fcn(self, *args, **kwargs)*
* File "/home/ruisun.hawaii/amber/amber18-gpu/updateutils/main.py", line
234, in _update_ambertools*
* last)*
* File "/home/ruisun.hawaii/amber/amber18-gpu/updateutils/main.py", line
49, in newfcn*
* fcn(self, *args, **kwargs)*
* File "/home/ruisun.hawaii/amber/amber18-gpu/updateutils/main.py", line
228, in _update_tree*
* first=localap.last() + 1, last=last, apply_=True)*
* File "/home/ruisun.hawaii/amber/amber18-gpu/updateutils/downloader.py",
line 108, in new_fcn*
* return fcn(*args, **kwargs)*
* File "/home/ruisun.hawaii/amber/amber18-gpu/updateutils/repos.py", line
287, in download_patches*
* os.path.join(self.destination.location, pname))*
* File "/home/ruisun.hawaii/amber/amber18-gpu/updateutils/downloader.py",
line 163, in download_to*
* dest.write(self.url.read(DL_CHUNK_SIZE))*
* File "/usr/lib64/python2.7/socket.py", line 380, in read*
* data = self._sock.recv(left)*
* File "/usr/lib64/python2.7/httplib.py", line 602, in read*
* s = self.fp.read(amt)*
* File "/usr/lib64/python2.7/socket.py", line 380, in read*
* data = self._sock.recv(left)*
*socket.error: [Errno 104] Connection reset by peer*
*Automatic patching failed! Check the errors before re-configuring*
I am at lost about how to solve this problem. Any help is greatly
appreciated.
Best wishes,
Rui
*Rui Sun*
Assistant Professor
Department of Chemistry
University of Hawaii at Manoa
Bilger 245B
2545 McCarthy Mall
Honolulu, HI 96822-2275
Phone: (808) 956-3207
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Received on Fri Dec 07 2018 - 02:00:02 PST
