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Re: [ESPResSo-users] espress0-3.2.0
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From: |
Stefan Kesselheim |
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Subject: |
Re: [ESPResSo-users] espress0-3.2.0 |
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Date: |
Wed, 5 Jun 2013 22:57:41 +0200 |
Hi Sonika,
thanks, I wanted just that mess.
It means you have successfully compiled Espresso!
Now comes the tricky thing how to use it!
You'll need a valid Espresso script, which you give as command line argument.
Probably the following will work:
./Espresso ./samples/lj_liquid.tcl
It will call Espresso using the lj_liquid example from the samples directory.
Take a look at lj_liquid.tcl: It is full of tcl-commands, of with some are
related to Espresso and some are ordinary tcl commands. You'll need to learn a
bit of the programming language tcl to be able to use Espresso.
Good luck!
Stefan
On Jun 5, 2013, at 10:51 PM, Sonika Gahlawat <address@hidden> wrote:
> I am sorry for this mess but the output goes something like…
>
> Last login: Wed Jun 5 14:51:09 on ttys000
> sonikas-macbook-pro:~ sonikagahlawat$ cd downloads
> sonikas-macbook-pro:downloads sonikagahlawat$ cd espresso-3.2.0
> sonikas-macbook-pro:espresso-3.2.0 sonikagahlawat$ ./configure
> checking build system type... x86_64-apple-darwin12.3.0
> checking host system type... x86_64-apple-darwin12.3.0
> checking target system type... x86_64-apple-darwin12.3.0
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... config/install-sh -c -d
> checking for gawk... no
> checking for mawk... no
> checking for nawk... no
> checking for awk... awk
> checking whether make sets $(MAKE)... yes
> checking whether to enable maintainer-specific portions of Makefiles... no
> checking whether make supports nested variables... yes
> checking whether we are using development sources... no
> ****************************************************************
> * Checking compiler characteristics and MPI support *
> ****************************************************************
> checking for style of include used by make... GNU
> checking whether to compile using MPI... yes
> checking for mpicc... no
> checking for hcc... no
> checking for mpxlc_r... no
> checking for mpxlc... no
> checking for mpcc... no
> checking for cmpicc... no
> checking for gcc... gcc
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking for gcc option to accept ISO C89... none needed
> checking dependency style of gcc... gcc3
> checking for library containing MPI_Init... no
> configure: WARNING: No MPI compiler found, will use fake implementation!
> checking whether the compiler accepts -O5... yes
> checking whether the compiler accepts -Wall... yes
> checking how to inline functions... static inline
> checking for gcc option to accept ISO C99... -std=gnu99
> checking for gcc -std=gnu99 option to accept ISO Standard C... (cached)
> -std=gnu99
> checking whether gcc -std=gnu99 and cc understand -c and -o together... yes
> checking for an ANSI C-conforming const... yes
> checking whether time.h and sys/time.h may both be included... yes
> ****************************************************************
> * Checking for programs *
> ****************************************************************
> checking for ranlib... ranlib
> checking for gawk... (cached) awk
> checking for grep that handles long lines and -e... /usr/bin/grep
> checking for egrep... /usr/bin/grep -E
> checking whether ln -s works... yes
> checking for doxygen... no
> checking for dot... no
> checking for pdflatex... /usr/texbin/pdflatex
> checking for makeindex... /usr/texbin/makeindex
> checking for bibtex... /usr/texbin/bibtex
> checking for python... /usr/bin/python
> checking whether python -B works... yes
> ****************************************************************
> * Checking for standard headers *
> ****************************************************************
> checking how to run the C preprocessor... gcc -std=gnu99 -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking arpa/inet.h usability... yes
> checking arpa/inet.h presence... yes
> checking for arpa/inet.h... yes
> checking fcntl.h usability... yes
> checking fcntl.h presence... yes
> checking for fcntl.h... yes
> checking float.h usability... yes
> checking float.h presence... yes
> checking for float.h... yes
> checking for inttypes.h... (cached) yes
> checking limits.h usability... yes
> checking limits.h presence... yes
> checking for limits.h... yes
> checking netdb.h usability... yes
> checking netdb.h presence... yes
> checking for netdb.h... yes
> checking netinet/in.h usability... yes
> checking netinet/in.h presence... yes
> checking for netinet/in.h... yes
> checking stddef.h usability... yes
> checking stddef.h presence... yes
> checking for stddef.h... yes
> checking for stdlib.h... (cached) yes
> checking for string.h... (cached) yes
> checking for strings.h... (cached) yes
> checking sys/file.h usability... yes
> checking sys/file.h presence... yes
> checking for sys/file.h... yes
> checking sys/socket.h usability... yes
> checking sys/socket.h presence... yes
> checking for sys/socket.h... yes
> checking sys/time.h usability... yes
> checking sys/time.h presence... yes
> checking for sys/time.h... yes
> checking for unistd.h... (cached) yes
> ****************************************************************
> * Checking for standard functions *
> ****************************************************************
> checking for stdlib.h... (cached) yes
> checking for GNU libc compatible malloc... yes
> checking for working memcmp... yes
> checking for stdlib.h... (cached) yes
> checking for GNU libc compatible realloc... yes
> checking sys/select.h usability... yes
> checking sys/select.h presence... yes
> checking for sys/select.h... yes
> checking for sys/socket.h... (cached) yes
> checking types of arguments for select... int,fd_set *,struct timeval *
> checking for size_t... yes
> checking for working strtod... yes
> checking for atexit... yes
> checking for floor... yes
> checking for getcwd... yes
> checking for gethostbyname... yes
> checking for memset... yes
> checking for pow... yes
> checking for rint... yes
> checking for select... yes
> checking for socket... yes
> checking for sqrt... yes
> ****************************************************************
> * Checking for required tools and libraries *
> ****************************************************************
> checking for libtcl8.6... no
> checking for libtcl8.5... yes
> checking for tcl.h... yes
> checking whether to use FFTW... guess
> checking for library containing fftw_plan_many_dft... no
> configure: WARNING: FFTW3 not found. Some features will not be available!
> checking whether to use CUDA... guess
> checking for nvcc... /usr/local/cuda/bin/nvcc
> checking for cudaGetDevice in -lcudart... no
> configure: WARNING: could not find cuda runtime library (cudart). Some
> features will not be available!
> checking for cufftPlan3d in -lcufft... no
> configure: WARNING: could not find cuda FFT library (cufft). Some features
> will not be available!
> checking whether CUDA compiles... no
> configure: WARNING: cannot compile CUDA code. Some features will not be
> available!
> checking whether CUDA runs... no
> configure: WARNING: cannot run CUDA code. Some features will not be available!
> ****************************************************************
> * Other settings *
> ****************************************************************
> checking whether to use efence... no
> checking the name of the configuration header... myconfig.h
> checking the number of available CPUs... 4
> ****************************************************************
> * Creating output files *
> ****************************************************************
> configure: creating ./config.status
> config.status: creating Makefile
> config.status: creating config/Makefile
> config.status: creating config/myconfig-sample-header.h
> config.status: creating src/Makefile
> config.status: creating tools/Makefile
> config.status: creating scripts/Makefile
> config.status: creating testsuite/Makefile
> config.status: creating testsuite/configs/Makefile
> config.status: creating doc/Makefile
> config.status: creating doc/logo/Makefile
> config.status: creating doc/ug/Makefile
> config.status: creating doc/dg/Makefile
> config.status: creating doc/doxygen/Makefile
> config.status: creating doc/tutorials/Makefile
> config.status: creating doc/tutorials/01-lennard_jones/Makefile
> config.status: creating doc/tutorials/02-charged_system/Makefile
> config.status: creating doc/latexit.sh
> config.status: creating testsuite/runtest.sh
> config.status: creating tools/es_mpiexec
> config.status: creating src/acconfig.h
> config.status: src/acconfig.h is unchanged
> config.status: executing depfiles commands
> config.status: executing myconfig-sample.h commands
> ****************************************************************
> * Configuration summary *
> ****************************************************************
> platform detected = x86_64-apple-darwin12.3.0
> package version = 3.2.0
> development sources = no
>
> Compiler
> --------
> compiler = gcc -std=gnu99
> linker =
> c compiler flags = -Wall -O5
> c preprocessor flags =
> linker flags =
> libraries = -ltcl8.5 -lm
> using debug flags =
> using profiling flags =
> inline =
>
> Libraries
> ---------
> Tcl version = tcl8.5
> Tk version = none
> FFTW = no
> efence = no
>
> Other settings
> --------------
> local config header = myconfig.h
> installation prefix = /Users/sonikagahlawat/Espresso
> number of test tasks = 4
> mympiexec =
> mpiexec =
> pdflatex = /usr/texbin/pdflatex
> makeindex = /usr/texbin/makeindex
> bibtex = /usr/texbin/bibtex
> doxygen = no
> dot =
> python = /usr/bin/python -B
>
> CUDA disabled or not supported.
> WARNING: MPI disabled or not supported! Parallelization turned off.
> sonikas-macbook-pro:espresso-3.2.0 sonikagahlawat$ make
> Making all in config
> make[1]: Nothing to be done for `all'.
> Making all in src
> -n Determining myconfig file...
> ../src/myconfig-default.h
> VERSION=`cd ..; sh config/genversion.sh -c`; \
> if ! test -e "config-version.c" || \
> test "$VERSION" != "`cat config-version.c`"; then \
> echo "$VERSION" > config-version.c; \
> fi
> make all-am
> -n Determining myconfig file...
> ../src/myconfig-default.h
> VERSION=`cd ..; sh config/genversion.sh -c`; \
> if ! test -e "config-version.c" || \
> test "$VERSION" != "`cat config-version.c`"; then \
> echo "$VERSION" > config-version.c; \
> fi
> Making all in .
> test -e Espresso || ln -s src/Espresso .
> Making all in scripts
> for file in init.tcl ABHmath.tcl auxiliary.tcl blockfile_support.tcl
> bundle.tcl countBonds.tcl dielectrics.tcl gibbs_ghmc.tcl
> parallel_tempering.tcl pdb.tcl polymer.tcl statistics.tcl vtf.tcl vtk.tcl
> object_in_fluid.tcl; do \
> if test ! -e $file || test ! $file -ef
> /Users/sonikagahlawat/downloads/espresso-3.2.0/scripts/$file; then \
> /usr/bin/install -c -m 644
> /Users/sonikagahlawat/downloads/espresso-3.2.0/scripts/$file
> /Users/sonikagahlawat/downloads/espresso-3.2.0/scripts; \
> fi; \
> done
> Making all in tools
> make[1]: Nothing to be done for `all'.
> Making all in testsuite
> Making all in configs
> for file in myconfig-empty.h myconfig-nofftw.h myconfig-compileonly.h
> myconfig-maxset.h myconfig-restcompile1.h myconfig-restcompile2.h
> myconfig-LB.h myconfig-LBGPU.h myconfig-tunableslip.h myconfig-adress.h; do \
> if ! test -e $file; then \
> ln -s ./$file .; \
> fi; \
> done
> Making all in .
> make[2]: Nothing to be done for `all-am'.
> Making all in doc
> Making all in logo
> make[2]: Nothing to be done for `all'.
> Making all in doxygen
> make[2]: Nothing to be done for `all'.
> Making all in dg
> make[2]: Nothing to be done for `all'.
> Making all in ug
> make[2]: Nothing to be done for `all'.
> Making all in tutorials
> Making all in 01-lennard_jones
> make[3]: Nothing to be done for `all'.
> Making all in 02-charged_system
> make[3]: Nothing to be done for `all'.
> make[3]: Nothing to be done for `all-am'.
> make[2]: Nothing to be done for `all-am'.
> sonikas-macbook-pro:espresso-3.2.0 sonikagahlawat$ ./Espresso
> *******************************************************
> * *
> * - ESPResSo - *
> * ============ *
> * A Parallel Molecular Dynamics Program *
> * *
> * (c) 2010,2011,2012,2013 *
> * The ESPResSo project *
> * *
> * (c) 2002,2003,2004,2005,2006,2007,2008,2009,2010 *
> * Max-Planck-Institute for Polymer Research *
> * Mainz, Germany *
> * *
> *******************************************************
>
> This is ESPResSo-3.2.0.
>
> ESPResSo is free software: you can redistribute it and/or modify
> it under the terms of the GNU General Public License as published by
> the Free Software Foundation, either version 3 of the License, or
> (at your option) any later version.
>
> ESPResSo is distributed in the hope that it will be useful,
> but WITHOUT ANY WARRANTY; without even the implied warranty of
> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> GNU General Public License for more details.
>
> You should have received a copy of the GNU General Public License
> along with this program. If not, see <http://www.gnu.org/licenses/>.
>
> % Espresso Scripts
> invalid command name "Espresso"
> % Scripts
> invalid command name "Scripts"
> %
>
> On Jun 5, 2013, at 3:28 PM, Stefan Kesselheim <address@hidden> wrote:
>
>> Hi,
>> so you probably did
>> ./configure
>> make
>> You'll need both commands to create an executable. The executable can be
>> started by
>> ./Espresso
>> Can you send us the output?
>> Cheers
>> Stefan
>>
>> On Jun 5, 2013, at 10:25 PM, Sonika Gahlawat <address@hidden> wrote:
>>
>>> But every time I give the command espresso scripts, I get no result. I am
>>> struggling to make espresso file.
>>>
>>> On Jun 5, 2013, at 3:22 PM, Stefan Kesselheim <address@hidden> wrote:
>>>
>>>> Hi Sonika,
>>>>
>>>> On Jun 5, 2013, at 8:46 PM, Sonika Gahlawat <address@hidden> wrote:
>>>>
>>>>>> I am trying to follow the steps in the user manual but I am getting the
>>>>>> warning " mpi not found or disabled" every time I prepare it for
>>>>>> configuration.
>>>>>> I have no clue how to proceed to the step of espresso scripts.
>>>>
>>>> This is not an error: It means that the mpi library necessary for parallel
>>>> execution is not found. You can use all features of Espresso without that,
>>>> note only that for some applications you can considerably speed up
>>>> calculations by using several CPU cores on a multicore computer, or on a
>>>> cluster architecture.
>>>> The message you obtained is merely a warning, that the parallel features
>>>> are not avail able. You can however compile Espresso by typing
>>>> make
>>>> and use it. Have fun!
>>>> If you want to use espresso in parallel make sure you have an mpi library
>>>> installed on your system. Your system administrator can probably help you
>>>> with that. All linux distributions allow to install e.g. openmpi through
>>>> the package managers.
>>>> Cheers
>>>> Steafn
>>>>
>>