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ECCE 6.3 - missing some components?
From NWChem
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| 10:07:16 AM PDT - Fri, Apr 27th 2012 |
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I just installed ecce-6.3 from the 32bit linux binaries onto a Ubuntu (32bit) virtual machine (VirtualBox under MacOS 10.7). I did the full install as user ecce (not root). Host was set to "localhost".
I'm hoping to test-drive ecce on this single desktop computer for the time being.
The server is running, and I can start ecce, but many of the "tools" described in the help are not present in the toolbar.
The only tools are organizer, builder, viewer, machine browser, periodic table, and then help,support,preferences, and windows stacked in a single tab.
So, I can build a simple molecule and save it as a pdb, xyz, etc. However, there was no obvious way to create an input file for nwchem. Clicking "help" brings up the help browser (for ecce 4, btw), and it's obvious the "calculation manager" would be a nice tool - but that's not one of my choices.
All the requisite software seemed to be in place when I ran the ecce installer, but there was an error on the console after starting ecce:
Failed to load module: /usr/lib/i386-linux-gnu/gio/modules/libgiolibproxy.so
Still, builder and machine browser seemed to work just fine.
It this is correct, then I'm at a loss as far as doing anything other than creating molecules and saving them. Is there a more current help document?
Or, if I'm actually missing components, how do I install them?
Thanks.
Don Berry
Dept. of Chemistry
University of Pennsylvania
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| 11:20:09 AM PDT - Fri, Apr 27th 2012 |
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Hi Don,
You have all the ECCE components (applications), but only some of them are accessible from our Gateway toolbar application. Those are the ones that make sense to start when you aren't in the "context" of a specific calculation (global tools would be another way of describing it). The Calculation Editor for instance requires you to be in the context of a calculation you have already created, although in this case it can be a brand new calculation where you haven't done anything yet like built/loaded a chemical system. Those other applications you are looking for including Calculation Editor, Basis Set Tool, and Job Launcher are started from the Organizer application. So you'll want to start the Organizer from the Gateway and then create a calculation (of type NWChem, Gaussian, etc.) using the options in the "File" menu and then ECCE will automatically select that newly created calculation in the Organizer. The right-hand pane will then display the icons for the others tools that can be invoked in the context of a calculation (they are also accessible from the Tools menu in Organizer). Those are the tools you are "missing". If you had created a molecular dynamics study instead of a calculation, then different tools would be available (e.g. MD Prepare Editor, MD Dynamics Editor, etc.). Same goes for a reaction study (e.g. Polyrate Editor, DirDyVTST Editor).
From the Organizer Help menu, select "On Organizer..." for some more information on how the Organizer works. The Organizer application is really the heart of ECCE when you use ECCE to setup and run calculations instead of just create molecules and look at NWChem output properties like many ECCE users do.
I think it's safe to ignore that missing "gio" shared library unless you find other issues and then we can revisit it. That's probably just an artifact of ECCE being built on a single operating system and hardware platform, but running it on a gamut of Linux platforms.
Gary
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| 2:19:08 PM PDT - Fri, Apr 27th 2012 |
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Thanks for the reply... in the meantime I read enough to figure out creating a new calculation under Organizer was the way to go. OTOH, it was not obvious at first HOW to create a new calc 
That is, my organizer window had no menus at the top, but a right-click brought up the contextual menu.
Unfortunately, I then got an error when I tried to start a new calc (in the bottom pane of the organizer window, something about not being able to complete the action.)
Since I was blundering my way through installing both the Virtual Ubuntu machine AND installing ECCE, I've taken the nuclear option and trashed the entire virtual machine and am restarting from scratch. I believe I have a better handle on the entire process and a clean install is the way to go.
Incidentally, for jollies I tried directly running the binary nwchem installed as part of the ECCE install. That is, from the command line (% ./ecce-v6.3/apps/bin...../nwchem test.nw)
Unfortunately I got an error about a missing gFortran shared library. I'm hoping installing gFortran in Ubuntu will resolve that.
Thanks again, and it's nice to know someone is reading these lists!
Don Berry
PS since I was about to delete the entire Ubuntu "box", I truly regret not typing the following, just to say I had done it:
cd /; sudo rm -rf *
Have a nice weekend.
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| 4:46:30 PM PDT - Fri, Apr 27th 2012 |
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Hi Don,
There is an Ubuntu bug with menubars! Any Gtk based application using menubars doesn't work right in recent releases. I found it with Ubuntu 11.10 and I assume you are using the latest 12.04. The menubars only show up the very first time you run an application and then will be gone from that point on. I understand it could be very confusing without menubars and there really is only a subset of operations you can do with the right mouse button context popup.
But, there is a workaround that has been documented by others to get menubars back if you do google searches related to wxWidgets (what ECCE uses) apps running on Ubuntu. You need to issue the following command and then you will see ECCE application menubars (definitely you can't do much with ECCE without them):
$ sudo apt-get remove appmenu-gtk
I documented this in our ECCE release for those building from source code, but I forgot to do it for the binary distributions. So just now I updated the INSTALL file in the top-level directory with this information--I know it's a bit odd because you have to do the install to extract all the files and get a README file, but I thought I would document it somewhere at least. Hopefully the Ubuntu developers get around to fixing this issue as no other Linux has this problem. In fact, in the notes for those building from a source code distribtuion I actually recommended that those who didn't have a need or preference for a certain Linux use something other than Ubuntu because of this. My recommendation from building/running ECCE on a variety of platforms is to use either Debian or Mint. Those were the nicest in my experience. The one to completely avoid for the present time at least is Fedora. I found multiple times that it would corrupt the operating system trying to install certain packages needed to build and run ECCE (and these are pretty common packages like gtk+-2.0, so it was pretty surprising). It's also surprising because Ubuntu is normally a pretty nice Linux to install and run so I would really recommend it other than this issue.
Also, you can't run NWChem directly without ECCE generating a wrapper job submit script precisely because of the problem you found with the missing gfortran shared library. I think another user had this issue and I replied here in the wiki to that. ECCE bundles the needed shared library and then our ECCE generated job submit script adds it to the $LD_LIBRARY_PATH. You could do that yourself if you really do want to run it from the command line without an ECCE submit script. I would just recommend running it the first time via ECCE and then you'll see how to set $LD_LIBRARY_PATH.
I see you also got an error trying to "start" a new calculation in the Organizer. Do you mean "create" rather than "start"? Why don't you go ahead and create a new VM (Ubuntu or otherwise), install ECCE again, do the fix for menubars, and then see if you still have the problem. Normally we only see failures like that when something strange is going on with file permissions for the ECCE data server and that would be unusual with a brand new ECCE install (tends to happen with "upgrade" type installs). Hopefully it will go away with a clean install, but let me know and I'm sure it's something that can be solved. Also try creating some project folders to see if it's a general problem that you can't write to the data server. I assume that you are in the context of your own "users" folder when you do that create. Definitely you will get an error if you try to create a calculation under a directory where you don't have write permission like one level up from your users folder.
Gary
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| 5:11:56 PM PDT - Fri, Apr 27th 2012 |
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Hi Gary,
update:
New VM built, packages added, ecce installed, server started...
While logged in as ecce, ran ecce, created NH3, ran nwchem, visualized results. Good news! NH3 is still C3v and stable.
Seemed strange to have to ssh in as myself to actually run the calc, but...
Logged in as another user, ran ecce, created a new project, then grew frustrated figuring out how to add a new calculation to that project, tried to save CH4.nw from the builder, got a core dump.
One thing is obvious: ECCE's paradigm is entirely non-obvious to me
That's my problem, not yours, so it's time for me to RTFM.
BTW, the "lack of menus" isn't nearly as terrible as I originally thought. They menus ARE present, but only in the bar of the "main window", just not in the various other windows where one might look for them. <shrug>
I'll read your response more carefully after I have dinner and some sleep, and then fix things.
Thanks again.
Don Berry
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| 8:07:19 PM PDT - Fri, Apr 27th 2012 |
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Hi Gary,
Fixing the menus was indeed trivial. Now things work better, and the process makes more sense.
FWIW, part of my confusion regarding the organizer vs. the calculation manager stems from the various help files and documentation available from the ECCE website. Much of it clearly refers to older versions.
For example, this page about the Organizer:
http://ecce.pnl.gov/about/manager.shtml
has a link labeled "ECCE help: Organizer"
that actually points to THIS page:
http://ecce.emsl.pnl.gov/cgi-bin/help/toolhelp?calcmgr
which is actually all about... the calculation manager.
That's enough to drive a new user slightly crazy.
As far as I can tell, the help pages (html) stored within the binary ecce distribution is NOT available externally (i.e. on ecce.pnl.gov). Pity, that.
Thanks.
Don
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Edited On 8:20:28 PM PDT - Fri, Apr 27th 2012 by Dberry
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| 11:43:31 AM PDT - Mon, Apr 30th 2012 |
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I commiserate with you on the state of the ECCE help system. ECCE hasn't been funded to provide a cohesive help system in many years. When we were, there were a couple of technical writers on the team who the developers worked with and it was quite nice. One bit of advice I'd give now is to not use the http://ecce.pnl.gov website (http://ecce.emsl.pnl.gov points to the same) when it comes to help on individual applications (the website is good for release notes and the movies we created demonstrating specific functionality). I'd stick to getting help from within ECCE itself realizing that even that is dated in many places.
The Organizer help was rewritten (as more of an overview rather than the previous detailed help) along with the Builder/Viewer and those are now "client-based" (file) help instead of via the web server even though it is displayed in a web browser. That's why the Organizer help on the ECCE website points to the old Calculation Manager application since we can't serve file based help from our web server (as you hypothesized). The Builder is the same although the name of the application wasn't changed in that case which potentially could lead to even more confusion. You have to use the applications themselves to see that help.
I just removed the online help links for the Organizer, Builder, and Viewer applications to hopefully be less misleading (no longer links to the old applications). Instead there are notes to see the help in the applications themselves. I left the other applications as they were, even though those too are out of date--just less so. When we converted from the old X Windows Motif toolkit GUIs to wxWidgets we did some enhancements to every application based on experience from our initial versions (and unfortunately also lost a minor feature here and there). But, the web-based help predates the wxWidgets conversion. The Organizer and Builder/Viewer got major redesigns and that's why they were the only ones to get an overview-level of new help.
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