[gmx-users] Problems in compiling GROMACS with VMD plugin (Roland Schulz)

Roland Schulz roland at utk.edu
Thu Jul 10 06:42:22 CEST 2014 

Hi,

are you building with shared-libs (BUILD_SHARED_LIBS=ON)? Is this on Linux?
Is GMX_USE_PLUGINS defined in config.h?

Roland


On Wed, Jul 9, 2014 at 6:15 AM, ming ma <morning22704 at gmail.com> wrote:

> 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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> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gromacs.org_gmx-users digest..."
> >
> >
> > 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.
> >
> >
> > End of gromacs.org_gmx-users Digest, Vol 123, Issue 49
> > ******************************************************
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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>
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>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309

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