On 8/21/15 11:18 AM, Atsutoshi Okabe wrote:
Thanks, Mark.
I inserted quotation in line 52 as Mark suggested.
I tried cmake again and got the only error.
Boost >= 1.44 not found. Using minimal internal version. This may cause trouble
if you plan on compiling/linking other software that uses Boost against GROMACS.
I don't know what the error means, but I did make and make install.
After finished, I checked /bin directory. But almost all commands which we need
to execute(i.g mdrun, trjconv...) were not generated.
Actually, onlyI the following file were generated in bin directory.
bin/
bin/xplor2gmx.pl
bin/GMXRC.bash
bin/gmx-completion-gmx_mpi.bash
bin/demux.pl
bin/GMXRC.zsh
bin/GMXRC
bin/gmx-completion.bash
bin/GMXRC.csh
bin/gmx_mpi
What causes this problem?
There is no problem. This is the new convention - one binary, called gmx (in
this case gmx_mpi since you compiled with MPI) and everything is a module of
that binary:
gmx grompp ...
gmx mdrun ...
(etc)
-Justin
2015/08/20 21:44、Mark Abraham <mark.j.abra...@gmail.com> のメール：
Hi,
You should change line 52 from what it is, to what I suggested - which
inserts quotation marks around one of the variable interpolations.
Mark
On Thu, Aug 20, 2015 at 2:43 PM 岡部篤俊 <atsutoshi0...@gmail.com> wrote:
Thanks, Peter.
But , I mean I don’t know what line I should change to from line 52 of
cmake/FindPhinx.cmake to solve this error.
Leucer
2015/08/20 16:02、Kroon, P.C. <p.c.kr...@rug.nl> のメール：
Just use your favourite text editor.
Peter
On Thu, Aug 20, 2015 at 3:10 AM, <atsutoshi0...@gmail.com> wrote:
Line 52 of cmake/FindSphinx.cmake file is written below.
string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
Can you tell me how I can change the line?
Bests,
Leucer
2015/08/19 23:11、Mark Abraham <mark.j.abra...@gmail.com> のメッセージ:
Hi,
On Wed, Aug 19, 2015 at 3:49 PM 岡部篤俊 <atsutoshi0...@gmail.com> wrote:
Hi,
I am unable to compile Gromamcs 5.1 using the following cmake
command.
cmake .. -DGMX_FFT_LIBRARY=fftpack
-DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off
-DGMX_THREAD_MPI=off -DGMX_MPI=on -DGMX_CPU_ACCELERATION=SSE4.1
Unrelated, but you now need to use -DGMX_SIMD=SSE4.1 to have the same
effect.
-DGMX_USE_RDTSCP=off
Then I got the error message.
Boost >= 1.44 not found. Using minimal internal version. This may
cause
trouble if you plan on compiling/linking other software that uses
Boost
against GROMACS.
CMake Error at cmake/FindSphinx.cmake:52 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments
total
to
command.
Call Stack (most recent call first):
docs/CMakeLists.txt:62 (find_package)
Could you advice what could be causing this error?
We try to find Sphinx in case people want to build the new
documentation,
but it looks like some part of the detection isn't reliable enough. Can
you
please try changing line 52 of cmake/FindSphinx.cmake to read
string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
and let us know how you go?
Mark
I was able to compile Gromacs 5.0 using same cmake command….
Bests,
Leucer
--
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-requ...@gromacs.org.
--
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-requ...@gromacs.org.
--
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-requ...@gromacs.org.
--
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-requ...@gromacs.org.
--
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-requ...@gromacs.org.
--
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-requ...@gromacs.org.
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
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-requ...@gromacs.org.
