[gmx-users] Problems in compiling GROMACS with VMD plugin (Roland Schulz)
ming ma
morning22704 at gmail.com
Wed Jul 9 12:15:50 CEST 2014
Hi Roland
Now I know how to reply more specifically. Here is the email I sent
yesterday :)
Thanks for your reply.
>> GMX_USE_PLUGINS has to be enabled in your CMackeCache.txt. Are you
building
>> under Linux? It probably didn't find dlopen support. Look for "Result of
>> test for dlopen" when you run cmake in a new build folder. You can see in
>> CMakeFiles/CMakeError.log why the dlopen test fails.
First, I need to apologize as I don't know how to reply to the contents
related to my questions only (my thread), so I just replied here directly.
First question, how can I enabled GMX_USE_PLUGINS? Intuitively, I edit the
file in gromacs-xxx/build/CMakeCache.txt manually by
setting GMX_USE_PLUGINS fro m OFF to ON.
However, it doesn't work. I first grep PLUGINS in CMakeCache.txt, and got
the following results
[ming at mingtlv myserial]$ grep PLUGINS CMakeCache.txt
GMX_LOAD_PLUGINS:BOOL=ON
//ADVANCED property for variable: GMX_LOAD_PLUGINS
GMX_LOAD_PLUGINS-ADVANCED:INTERNAL=1
GMX_USE_PLUGINS:INTERNAL=OFF
>From the last line, it seems that GROMACS didn't build with PLUGINS, though
the first one is ON.
Then I grepped dlopen, DLOPEN, vmd, VMD, PLUGINS, plugins in both
CMakeFiles/CMakeError.log and found nothing.
In the output of cmake, I found the following things for dlopen, DLOPEN and
vmd.
[ming at mingtlv gromacs-4.6.5]$ grep dlopen s.log
-- Checking for dlopen
-- Checking for dlopen - found
[ 3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmddlopen.c.o
[ming at mingtlv gromacs-4.6.5]$ grep DLOPEN s.log
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
[ming at mingtlv gromacs-4.6.5]$ grep vmd s.log
[ 3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmddlopen.c.o
[ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmdio.c.o
So, I still have no idea what's the problem.... Any suggestions?
Best
Ming
2014-07-08 21:34 GMT+03:00 <
gromacs.org_gmx-users-request at maillist.sys.kth.se>:
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> Today's Topics:
>
> 1. Re: gmx-5.0 features (Szil?rd P?ll)
> 2. Re: gmx-5.0 features (Szil?rd P?ll)
> 3. Re: hardware setup for gmx (Szil?rd P?ll)
> 4. Re: hardware setup for gmx (Szil?rd P?ll)
> 5. Re: strange but true : How to explain and avoid? (Justin Lemkul)
> 6. Re: Problems in compiling GROMACS with VMD plugin (Roland Schulz)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 8 Jul 2014 19:25:42 +0200
> From: Szil?rd P?ll <pall.szilard at gmail.com>
> To: gmx-users at gromacs.org, Michael Brunsteiner <mbx0009 at yahoo.com>
> Cc: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] gmx-5.0 features
> Message-ID:
> <CAPZiCymXPUdbf-dVKSfBHn3sDR6u9KfQ7pPHAG1q==
> EgxQ8qvA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Thu, Jul 3, 2014 at 4:05 PM, Michael Brunsteiner <mbx0009 at yahoo.com>
> wrote:
>
> >
> >
> > Hi,
> >
> > I am sorry in case I overlooked the answers in the release-notes,
> > but I didn't find there answers to:
> > 1) does gmx-5.0 support free energy calculations + GPU ?
> >
>
> Yes.
>
>
> >
> > 2) does gmx-5.0 support double precision + GPU ?
> >
>
> No.
>
> Cheers,
> --
> Szil?rd
>
>
> >
> > cheers
> > michael
> >
> > ===============================
> >
> >
> > Why be happy when you could be normal?
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> P?ll Szil?rd
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 8 Jul 2014 19:25:42 +0200
> From: Szil?rd P?ll <pall.szilard at gmail.com>
> To: gmx-users at gromacs.org, Michael Brunsteiner <mbx0009 at yahoo.com>
> Cc: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] gmx-5.0 features
> Message-ID:
> <CAPZiCymXPUdbf-dVKSfBHn3sDR6u9KfQ7pPHAG1q==
> EgxQ8qvA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Thu, Jul 3, 2014 at 4:05 PM, Michael Brunsteiner <mbx0009 at yahoo.com>
> wrote:
>
> >
> >
> > Hi,
> >
> > I am sorry in case I overlooked the answers in the release-notes,
> > but I didn't find there answers to:
> > 1) does gmx-5.0 support free energy calculations + GPU ?
> >
>
> Yes.
>
>
> >
> > 2) does gmx-5.0 support double precision + GPU ?
> >
>
> No.
>
> Cheers,
> --
> Szil?rd
>
>
> >
> > cheers
> > michael
> >
> > ===============================
> >
> >
> > Why be happy when you could be normal?
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> P?ll Szil?rd
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 8 Jul 2014 19:47:42 +0200
> From: Szil?rd P?ll <pall.szilard at gmail.com>
> To: gmx-users at gromacs.org, Michael Brunsteiner <mbx0009 at yahoo.com>
> Cc: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] hardware setup for gmx
> Message-ID:
> <
> CAPZiCymu2Zk68c2ZB4x45_jOHGFnRj6gF5h5-bB6AUkRhTuSGA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Please have a look at the gmx-users history, there has been recent
> discussions about this topic.
>
> Brief answer:
> * If you only/mostly run GROMACS using GPU, Intel CPUs with many fast cores
> combined with high-end Geforce GTX cards will give the best performance/$;
> e.g. currently i7 4930K + GTX 770,780 is what I would recommend
> * The ideal hardware balance depends on the kind of simulations you plan to
> do (e.g. system size, cut-off, #of concurrent simulations, etc.).
>
> Note however, that you could get much better perf/buck on e.g. AMD CPUs
> with middle-range GTX cards e.g. if you have many small simulations to run
> concurrently (and especially if you want rack-mountable OEM servers).
>
> Cheers,
>
>
> On Thu, Jul 3, 2014 at 3:46 PM, Michael Brunsteiner <mbx0009 at yahoo.com>
> wrote:
>
> >
> >
> > Hi,
> >
> > can anybody recommend a hardware setup to perform MD runs (with PME) that
> > has a good
> > price-performance ratio? ... in particular I'd be interested in learning
> > which combinations
> > of CPU and GPU can be expected to provide a good FLOPS-per-dollar ratio
> > with the more
> > recent gmx versions (4.6 or 5.0)?
> >
> > thanks in advance for any recommendations!
> >
> > Michael
> >
> >
> >
> > ps: if your opinion is highly subjective and/or perhaps prone to make
> > particular hardware vendors
> > really sad, you might want to send your answer only to my email rather
> > than to all gmx-users)
> >
> >
> >
> > ===============================
> > Why be happy when you could be normal?
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> P?ll Szil?rd
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 8 Jul 2014 19:47:42 +0200
> From: Szil?rd P?ll <pall.szilard at gmail.com>
> To: gmx-users at gromacs.org, Michael Brunsteiner <mbx0009 at yahoo.com>
> Cc: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] hardware setup for gmx
> Message-ID:
> <
> CAPZiCymu2Zk68c2ZB4x45_jOHGFnRj6gF5h5-bB6AUkRhTuSGA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Please have a look at the gmx-users history, there has been recent
> discussions about this topic.
>
> Brief answer:
> * If you only/mostly run GROMACS using GPU, Intel CPUs with many fast cores
> combined with high-end Geforce GTX cards will give the best performance/$;
> e.g. currently i7 4930K + GTX 770,780 is what I would recommend
> * The ideal hardware balance depends on the kind of simulations you plan to
> do (e.g. system size, cut-off, #of concurrent simulations, etc.).
>
> Note however, that you could get much better perf/buck on e.g. AMD CPUs
> with middle-range GTX cards e.g. if you have many small simulations to run
> concurrently (and especially if you want rack-mountable OEM servers).
>
> Cheers,
>
>
> On Thu, Jul 3, 2014 at 3:46 PM, Michael Brunsteiner <mbx0009 at yahoo.com>
> wrote:
>
> >
> >
> > Hi,
> >
> > can anybody recommend a hardware setup to perform MD runs (with PME) that
> > has a good
> > price-performance ratio? ... in particular I'd be interested in learning
> > which combinations
> > of CPU and GPU can be expected to provide a good FLOPS-per-dollar ratio
> > with the more
> > recent gmx versions (4.6 or 5.0)?
> >
> > thanks in advance for any recommendations!
> >
> > Michael
> >
> >
> >
> > ps: if your opinion is highly subjective and/or perhaps prone to make
> > particular hardware vendors
> > really sad, you might want to send your answer only to my email rather
> > than to all gmx-users)
> >
> >
> >
> > ===============================
> > Why be happy when you could be normal?
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> P?ll Szil?rd
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 08 Jul 2014 12:47:25 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] strange but true : How to explain and avoid?
> Message-ID: <53BC209D.8000809 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 7/8/14, 12:44 PM, Chetan Mahajan wrote:
> > Hi Tsjerk,
> >
> > Thanks. I get it. So in verision 4.6.5, adding 2>/dev/null at the end of
> > the command seems the only way out, since, as I said, I am also getting
> > greeting messages in addition to gcq quotes. However, adding
> 2>/dev/null will
> > also suppress unusual errors, if any at all. There does not seem a way
> out
> > of this.
> >
>
> Is there a reason these quotes or messages are causing a problem? If
> you're
> simply dumping to a text file, a simple grep -v "gcq" will get rid of the
> quotes
> lines and you can continue doing whatever you were doing before.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 8 Jul 2014 14:33:54 -0400
> From: Roland Schulz <roland at utk.edu>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Cc: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Problems in compiling GROMACS with VMD plugin
> Message-ID:
> <CAO2Twbk=mB3BTtCuA13nkqf=
> p1qwv381kAA9O_wm1BhF7+oXUQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> GMX_USE_PLUGINS has to be enabled in your CMackeCache.txt. Are you building
> under Linux? It probably didn't find dlopen support. Look for "Result of
> test for dlopen" when you run cmake in a new build folder. You can see in
> CMakeFiles/CMakeError.log why the dlopen test fails.
>
> Roland
>
>
> On Tue, Jul 8, 2014 at 10:27 AM, ming ma <morning22704 at gmail.com> wrote:
>
> > Hi,
> >
> > I met some problems in compiling GROMACS with VMD plugin. Generally
> > speaking, the compilation is finished, but it did't involve vmd plugin.
> >
> > I first complied the serial version of GROMACS, the VMDDIR is set as
> >
> > export VMDDIR=/home/ming/lib/vmd191
> >
> > where vmd is installed,
> >
> > [ming at mingtlv vmd191]$ pwd
> > /home/ming/lib/vmd191
> > [ming at mingtlv vmd191]$ ls
> > Announcement libexpat.so.0 plugins shaders
> > tachyon_LINUXAMD64
> > doc libsqlite3.so.0 README stride_LINUXAMD64
> > vmd_completion.dat
> > libcudart.so.4 LICENSE scripts surf_LINUXAMD64
> vmd_LINUXAMD64
> >
> > , then I complied GROMACS successfully. Then I set the VMD_PLUGIN_PATH
> >
> > [ming at mingtlv g-van]$ echo $VMD_PLUGIN_PATH
> > /home/ming/lib/vmd191/plugins/LINUXAMD64/molfile
> >
> > however, when I trying to use g_vanhove to load a LAMMPS trajectory with
> >
> > g_vanhove -f ../traj.lammpstrj -s topol.tpr -om vanhove.xpm -rmax 20
> -rbin
> > 0.1
> >
> > I met the following problem,
> >
> > Program g_vanhove, VERSION 4.6.5
> > Source code file: /home/ming/software/gromacs-4.6.5/src/gmxlib/trxio.c,
> > line: 1040
> >
> > Fatal error:
> > Not supported in read_first_frame: ../traj.lammpstrj. Please make sure
> that
> > the file is a trajectory.
> > GROMACS is not compiled with plug-in support. Thus it cannot read
> > non-GROMACS trajectory formats using the VMD plug-ins.
> > Please compile with plug-in support if you want to read non-GROMACS
> > trajectory formats.
> >
> > So it seems that GROMACS was not compiled with the vmd plugin. For
> example,
> > in the compiling_directory/src/config.h, I can't find GMX_DLOPEN, and in
> > the output of the compilation, by searching for vmd and VMD, I can only
> > find lines
> >
> > [ 3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmddlopen.c.o
> > ....
> > [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmdio.c.o
> >
> >
> > Sorry anybody have ideas how I can solve this problem?
> >
> > Best
> > Ming
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
>
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