Dear Sun.
Have you installed the other packages as suggested in manual :
1.try this for ubuntu :
sudo apt-get install bc csh flex gfortran g++ xorg-dev \
zlib1g-dev libbz2-dev patch
or if you're using centos/redhat
1. sudo yum install gcc gcc-gfortran gcc-c++ flex tcsh zlib-devel \
bzip2-devel libXt-devel libXext-devel libXdmcp-devel \
tkinter openmpi openmpi-devel perl perl-ExtUtils-MakeMaker \
patch bison boost-devel
For clarity on this check our :
http://ambermd.org/Installation.php
http://jswails.wikidot.com/installing-ambertools-14-and-older-amber
If this is went successfully, follow it with ./configure gpu
This is assuming that your GPU drivers and supports are installed correctly.
On Fri, Dec 7, 2018 at 6:32 PM Rui Sun <ruisun.hawaii.edu> wrote:
>
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 07 2018 - 03:00:01 PST
