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HomerReid / scuff-em

A comprehensive and full-featured computational physics suite for boundary-element analysis of electromagnetic scattering, fluctuation-induced phenomena (Casimir forces and radiative heat transfer), nanophotonics, RF device engineering, electrostatics, and more. Includes a core library with C++ and python APIs as well as many command-line applications.
http://www.homerreid.com/scuff-em
GNU General Public License v2.0
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Missing scanner.c #105

Closed Issachooi closed 7 years ago

Issachooi commented 7 years ago

Dear Homer Reid,

Here is the subsequent problem that I face during the installation of Scuff-em.

hooi0004@hooi0004-HP-Z400-Workstation:~/scuff-em$ sudo make install Making install in src make[1]: Entering directory '/home/hooi0004/scuff-em/src' Making install in libs make[2]: Entering directory '/home/hooi0004/scuff-em/src/libs' Making install in libhrutil make[3]: Entering directory '/home/hooi0004/scuff-em/src/libs/libhrutil' make[4]: Entering directory '/home/hooi0004/scuff-em/src/libs/libhrutil' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/usr/local/include/scuff-em' /usr/bin/install -c -m 644 libhrutil.h '/usr/local/include/scuff-em' make[4]: Leaving directory '/home/hooi0004/scuff-em/src/libs/libhrutil' make[3]: Leaving directory '/home/hooi0004/scuff-em/src/libs/libhrutil' Making install in libhmat make[3]: Entering directory '/home/hooi0004/scuff-em/src/libs/libhmat' make install-am make[4]: Entering directory '/home/hooi0004/scuff-em/src/libs/libhmat' make[5]: Entering directory '/home/hooi0004/scuff-em/src/libs/libhmat' make[5]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/usr/local/include/scuff-em' /usr/bin/install -c -m 644 libhmat.h '/usr/local/include/scuff-em' make[5]: Leaving directory '/home/hooi0004/scuff-em/src/libs/libhmat' make[4]: Leaving directory '/home/hooi0004/scuff-em/src/libs/libhmat' make[3]: Leaving directory '/home/hooi0004/scuff-em/src/libs/libhmat' Making install in libSGJC make[3]: Entering directory '/home/hooi0004/scuff-em/src/libs/libSGJC' make[4]: Entering directory '/home/hooi0004/scuff-em/src/libs/libSGJC' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/usr/local/include/scuff-em' /usr/bin/install -c -m 644 libSGJC.h '/usr/local/include/scuff-em' make[4]: Leaving directory '/home/hooi0004/scuff-em/src/libs/libSGJC' make[3]: Leaving directory '/home/hooi0004/scuff-em/src/libs/libSGJC' Making install in libMDInterp make[3]: Entering directory '/home/hooi0004/scuff-em/src/libs/libMDInterp' make[4]: Entering directory '/home/hooi0004/scuff-em/src/libs/libMDInterp' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/usr/local/include/scuff-em' /usr/bin/install -c -m 644 libMDInterp.h '/usr/local/include/scuff-em' make[4]: Leaving directory '/home/hooi0004/scuff-em/src/libs/libMDInterp' make[3]: Leaving directory '/home/hooi0004/scuff-em/src/libs/libMDInterp' Making install in libMatProp make[3]: Entering directory '/home/hooi0004/scuff-em/src/libs/libMatProp' Making install in cmatheval make[4]: Entering directory '/home/hooi0004/scuff-em/src/libs/libMatProp/cmatheval' test -f scanner.c || /bin/bash ../../../../ylwrap scanner.l .c scanner.c -- /bin/bash /home/hooi0004/scuff-em/missing flex
lex.yyscanner.c is unchanged /bin/bash ../../../../libtool --tag=CC --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../../.. -I/usr/include/hdf5/serial/ -L/usr/lib/x86_64-linux-gnu/hdf5/serial/lib -g -O2 -fopenmp -pthread -g -O2 -MT scanner.lo -MD -MP -MF .deps/scanner.Tpo -c -o scanner.lo scanner.c libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../../.. -I/usr/include/hdf5/serial/ -L/usr/lib/x86_64-linux-gnu/hdf5/serial/lib -g -O2 -fopenmp -pthread -g -O2 -MT scanner.lo -MD -MP -MF .deps/scanner.Tpo -c scanner.c -fPIC -DPIC -o .libs/scanner.o g++: error: scanner.c: No such file or directory g++: fatal error: no input files compilation terminated. Makefile:508: recipe for target 'scanner.lo' failed make[4]: * [scanner.lo] Error 1 make[4]: Leaving directory '/home/hooi0004/scuff-em/src/libs/libMatProp/cmatheval' Makefile:521: recipe for target 'install-recursive' failed make[3]: * [install-recursive] Error 1 make[3]: Leaving directory '/home/hooi0004/scuff-em/src/libs/libMatProp' Makefile:385: recipe for target 'install-recursive' failed make[2]: * [install-recursive] Error 1 make[2]: Leaving directory '/home/hooi0004/scuff-em/src/libs' Makefile:382: recipe for target 'install-recursive' failed make[1]: * [install-recursive] Error 1 make[1]: Leaving directory '/home/hooi0004/scuff-em/src' Makefile:432: recipe for target 'install-recursive' failed make: *\ [install-recursive] Error 1

I do appreciate your help. Thanks alot.

Best Regards Chee Quen

Issachooi commented 7 years ago

When I use "make" instead of "sudo make install", the following appears:

hooi0004@hooi0004-HP-Z400-Workstation:~/scuff-em$ make make all-recursive make[1]: Entering directory '/home/hooi0004/scuff-em' Making all in src make[2]: Entering directory '/home/hooi0004/scuff-em/src' Making all in libs make[3]: Entering directory '/home/hooi0004/scuff-em/src/libs' Making all in libhrutil make[4]: Entering directory '/home/hooi0004/scuff-em/src/libs/libhrutil' /bin/bash ../../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../.. -I/usr/include/hdf5/serial/ -L/usr/lib/x86_64-linux-gnu/hdf5/serial/lib -g -O2 -fopenmp -pthread -MT libhrutil.lo -MD -MP -MF .deps/libhrutil.Tpo -c -o libhrutil.lo libhrutil.cc rm: cannot remove '.libs/libhrutil.o': Permission denied libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../.. -I/usr/include/hdf5/serial/ -L/usr/lib/x86_64-linux-gnu/hdf5/serial/lib -g -O2 -fopenmp -pthread -MT libhrutil.lo -MD -MP -MF .deps/libhrutil.Tpo -c libhrutil.cc -fPIC -DPIC -o .libs/libhrutil.o Assembler messages: Fatal error: can't create .libs/libhrutil.o: Permission denied Makefile:473: recipe for target 'libhrutil.lo' failed make[4]: * [libhrutil.lo] Error 1 make[4]: Leaving directory '/home/hooi0004/scuff-em/src/libs/libhrutil' Makefile:385: recipe for target 'all-recursive' failed make[3]: * [all-recursive] Error 1 make[3]: Leaving directory '/home/hooi0004/scuff-em/src/libs' Makefile:382: recipe for target 'all-recursive' failed make[2]: * [all-recursive] Error 1 make[2]: Leaving directory '/home/hooi0004/scuff-em/src' Makefile:432: recipe for target 'all-recursive' failed make[1]: * [all-recursive] Error 1 make[1]: Leaving directory '/home/hooi0004/scuff-em' Makefile:364: recipe for target 'all' failed make: *\ [all] Error 2 hooi0004@hooi0004-HP-Z400-Workstation:~/scuff-em$

Best Regards Chee Quen

HomerReid commented 7 years ago

The make is failing because by default it attempts to install to system-wide directories for which you need root access.

To get around this, use the --prefix argument to configure to specify an installation directory to which you have write access. For example, try

% configure --prefix=${HOME}/scuff-em-installation
% make install
Issachooi commented 7 years ago

Dear Homer Reid,

I typed in this: ./configure --prefix=/home/hooi0004/scuff-em-installation --with-hdf5-libdir=/usr/lib/x86_64-linux-gnu/hdf5/serial/lib --with-hdf5-includedir=/usr/include/hdf5/serial/

followed by sudo make install

It then showed: ... ... make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/home/hooi0004/scuff-em/interactiveTests' make[1]: Leaving directory '/home/hooi0004/scuff-em/interactiveTests' Making install in m4 make[1]: Entering directory '/home/hooi0004/scuff-em/m4' make[2]: Entering directory '/home/hooi0004/scuff-em/m4' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/home/hooi0004/scuff-em/m4' make[1]: Leaving directory '/home/hooi0004/scuff-em/m4' make[1]: Entering directory '/home/hooi0004/scuff-em' make[2]: Entering directory '/home/hooi0004/scuff-em' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/home/hooi0004/scuff-em' make[1]: Leaving directory '/home/hooi0004/scuff-em'

Does it imply that scuff-em is properly installed?

Best Regards Chee Quen

Issachooi commented 7 years ago

Meanwhile, a scuff-em-installation folder is created in /home

Issachooi commented 7 years ago

And I tried to run the program by:

scuff-analyze --mesh RoundedBeamUnitCell_192.msh. It return:

scuff-analyze: command not found

Is scuff-em not properly installed?

HomerReid commented 7 years ago

Does it imply that scuff-em is properly installed?

yes

scuff-analyze: command not found

since you installed the code to /home/hooi0004/scuff-em, the executables are installed in /home/hooi0004/scuff-em/bin, and there are two ways to communicate this information to the shell when running one of the executables:

% /home/hooi0004/scuff-em/bin/scuff-analyze --mesh RoundedBeamUnitCell_192.msh
% export PATH=${PATH}:/home/hooi0004/scuff-em/bin
% scuff-analyze --mesh RoundedBeamUnitCell_192.msh
Issachooi commented 7 years ago

Dear Homer Reid,

I appreciate your support and guidance so much, and I feel extremely thankful for your contribution in this field.

I will be using scuff-em mainly for the evaluation of Casimir forces in graphene system.

Best Regards Chee Quen

HomerReid commented 7 years ago

I'm glad it's working. If you are satisfied with the resolution of your questions, please close the issues.