Re: [Meep-discuss] installing parallel hdf5 into nonstanda rd directory
Here I attached the config.log for hdf5 for the above problem. Seong Kyu Kim - Original Message - From: Seong Kyu Kim [EMAIL PROTECTED] To: meep-discuss@ab-initio.mit.edu Date: 2008-05-14 11:51:16 Subject: [Meep-discuss] installing parallel hdf5 into nonstandard directory Dear prof. Steven G. Johnson and many other meep helpers. This January, I myself successfully installed the meep into a single processor Linux PC, which I have a root privilege. I have run some small ctl files O.K. for a month. Now, I am installing mpi version of the programs into a cluster system, which I do not have a root privilege. So I had to install all files into a nonstandard directory /home/skkim/local instead of the standard /usr/local. The biggest difficulty I have is to set the path for sharing libraries. Previously, I edited /etc/ld.so.conf to include a line /usr/local/lib, and this made sharing libraries so easy. But without the root privilege, I cannot do it in the cluster PC. I tried the following ways. (1) I made sure that guile.x86_64 and guile-devel.x86_64 were installed. (2) For the mpi, I made sure that mpiblast.x86_64, mpich-ethernet-gnu.x86_64 , openmpi.x86_64 , openmpi-devel.x86_64 , openmpi-libs.x86_64 were installed. (3) In my .cshrc file, I added the following lines, setenv LDFLAGS -L/home/skkim/local/lib setenv CPPFLAGS -I/home/skkim/local/include setenv LD_LIBRARY_PATH home/skkim/local/lib setenv LD_RUN_PATH /home/skkim/local/lib and modified the path, set path = (. $HOME/bin $HOME/local/bin $path) (4) I successfully installed libctl-3.0.3 into /home/skkim/local and its daughter directories. (5) I tried to install parallel hdf5 (version 1.8.0) with following commands; % setenv CC /usr/local/mpich/bin/mpicc % setenv CXX /usr/local/mpich/bin/mpicc % ./configure --prefix=$HOME/local % make all % make install The series of commands seemed to work fine, creating hdf5-related files in /home/skkim/local/lib, /home/skkim/local/bin. (However, it did not produce /home/skkim/local/doc.) (6) I tried to install h5utils (version-1.11.1) by typing; % ./configure --prefix=$HOME/local It gave configure: error: hdf5 libraries are required for compilation at the end of message display. When I typed % make all, it gave a whole bunch of error messages implying hdf5 is not found. Can someone help me with this problem? Seong Kyu Kim, professor Department of Chemistry Sungkyunkwan University Suwon, 440-746 Korea ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
Re: [Meep-discuss] installing parallel hdf5 into nonstandard directory
Message: 6 Date: Thu, 15 May 2008 00:13:42 +0900 From: Seong Kyu Kim [EMAIL PROTECTED] Subject: Re: [Meep-discuss] installing parallel hdf5 into nonstandard directory To: meep-discuss@ab-initio.mit.edu Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=euc-kr Here I attached the config.log for hdf5 for the above problem. Seong Kyu Kim - Original Message - From: Seong Kyu Kim [EMAIL PROTECTED] To: meep-discuss@ab-initio.mit.edu Date: 2008-05-14 11:51:16 Subject: [Meep-discuss] installing parallel hdf5 into nonstandard directory Dear prof. Steven G. Johnson and many other meep helpers. This January, I myself successfully installed the meep into a single processor Linux PC, which I have a root privilege. I have run some small ctl files O.K. for a month. Now, I am installing mpi version of the programs into a cluster system, which I do not have a root privilege. So I had to install all files into a nonstandard directory /home/skkim/local instead of the standard /usr/local. The biggest difficulty I have is to set the path for sharing libraries. Previously, I edited /etc/ld.so.conf to include a line /usr/local/lib, and this made sharing libraries so easy. But without the root privilege, I cannot do it in the cluster PC. I tried the following ways. (1) I made sure that guile.x86_64 and guile-devel.x86_64 were installed. (2) For the mpi, I made sure that mpiblast.x86_64, mpich-ethernet- gnu.x86_64 , openmpi.x86_64 , openmpi-devel.x86_64 , openmpi- libs.x86_64 were installed. (3) In my .cshrc file, I added the following lines, setenv LDFLAGS -L/home/skkim/local/lib setenv CPPFLAGS -I/home/skkim/local/include setenv LD_LIBRARY_PATH home/skkim/local/lib setenv LD_RUN_PATH /home/skkim/local/lib and modified the path, set path = (. $HOME/bin $HOME/local/bin $path) (4) I successfully installed libctl-3.0.3 into /home/skkim/local and its daughter directories. (5) I tried to install parallel hdf5 (version 1.8.0) with following commands; % setenv CC /usr/local/mpich/bin/mpicc % setenv CXX /usr/local/mpich/bin/mpicc % ./configure --prefix=$HOME/local % make all % make install The series of commands seemed to work fine, creating hdf5-related files in /home/skkim/local/lib, /home/skkim/local/bin. (However, it did not produce /home/skkim/ local/doc.) (6) I tried to install h5utils (version-1.11.1) by typing; % ./configure --prefix=$HOME/local It gave configure: error: hdf5 libraries are required for compilation at the end of message display. When I typed % make all, it gave a whole bunch of error messages implying hdf5 is not found. Can someone help me with this problem? Hi, I had a similar problem a couple of weeks ago with h5utils and parallel hdf5 libraries on my Mac. It can be fixed, or was fixed in my case, by adding this to the configure flags in addition to your other ones: CC=mpicc I think this tells the configure script/compiler to be expecting parallel libraries instead of serial ones. Hope this helps. Regards, Ian --- Research PhD Student Photonics Group Dept. of Electrical Electrical Engineering University of Bristol Rm 2.11, Queen's Building University Walk Bristol BS8 1TR email: [EMAIL PROTECTED] ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
[Meep-discuss] localized mode
Good night Steven . Thank you for your previous response about, how can transmission at photonic crystal larger than one. I have read some literatures about localized mode, which you said about. According to a book by J.M. Lourtioz, it can happen because with crystal in computation, the amplitude of wave will be larger. In some books and journal, including book by Joannopoulos and you, there is a termsurface state . I am wondering if this is the same thing with localized mode About localized mode, I want to know how to minimize its effect in transmission calculation. Is it by changing source position , or flux area position? My last question is about why the effect of localized mode is significant in low frequency? Is there any way to compute surface state and surface mode, by MPB or Meep?? slab2_s.ctl Description: Binary data ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
Re: [Meep-discuss] installing parallel hdf5 into nonstanda rd directory
I tried ./configure --prefix=$HOME/local CC=mpicc in compiling both hdf5 and h5utils in addition to commands in the above. But still it did not work. Here are lsome ines of messages when I type make after ./configure --prefix=$HOME/local CC=mpicc to complie for h5utils. make all-am make[1]: Entering directory `/home/skkim/Download/h5utils-1.11.1' /usr/local/mpich/bin/mpicc -DHAVE_CONFIG_H -I. -I/usr/skkim/local/include -g -O2 -MT arrayh5.o -MD -MP -MF .deps/arrayh5.Tpo -c -o arrayh5.o arrayh5.c arrayh5.c:29:18: hdf5.h: No such file or directory arrayh5.c: In function `arrayh5_create_withdata': arrayh5.c:55: error: `stderr' undeclared (first use in this function) arrayh5.c:55: error: (Each undeclared identifier is reported only once arrayh5.c:55: error: for each function it appears in.) arrayh5.c: In function `arrayh5_transpose': arrayh5.c:137: error: `stderr' undeclared (first use in this function) arrayh5.c: In function `arrayh5_getrange': arrayh5.c:153: error: `stderr' undeclared (first use in this function) arrayh5.c: At top level: arrayh5.c:163: error: syntax error before find_dataset arrayh5.c:163: error: syntax error before group_id arrayh5.c: In function `find_dataset': arrayh5.c:165: error: `d' undeclared (first use in this function) arrayh5.c:166: error: `H5G_stat_t' undeclared (first use in this function) arrayh5.c:166: error: syntax error before info arrayh5.c:168: error: `group_id' undeclared (first use in this function) arrayh5.c:168: error: `name' undeclared (first use in this function) arrayh5.c:168: error: `info' undeclared (first use in this function) arrayh5.c:169: error: `H5G_DATASET' undeclared (first use in this function) arrayh5.c:170: error: `stderr' undeclared (first use in this function) Thanks in advance. S.K. Kim - Hi, I had a similar problem a couple of weeks ago with h5utils and parallel hdf5 libraries on my Mac. It can be fixed, or was fixed in my case, by adding this to the configure flags in addition to your other ones: CC=mpicc I think this tells the configure script/compiler to be expecting parallel libraries instead of serial ones. Hope this helps. Regards, Ian --- Research PhD Student Photonics Group Dept. of Electrical Electrical Engineering University of Bristol Rm 2.11, Queen's Building University Walk Bristol BS8 1TR___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
Re: [Meep-discuss] installing parallel hdf5 into nonstanda rd directory
The problem I raised is now solved in a strange way. For the reason I do not still understand setenv LDFLAGS -L/home/skkim/local/lin and setenv CPPFLAGS -I/home/skkim/local/include should be typed before I type ./configure statement for h5utils. Putting in .cshrc was not enough. Seong Kyu Kim - Original Message - From: Seong Kyu Kim [EMAIL PROTECTED] To: meep-discuss@ab-initio.mit.edu Date: 2008-05-15 04:30:17 Subject: Re: [Meep-discuss]installing parallel hdf5 into nonstandard directory I tried ./configure --prefix=$HOME/local CC=mpicc in compiling both hdf5 and h5utils in addition to commands in the above. But still it did not work. Here are lsome ines of messages when I type make after ./configure --prefix=$HOME/local CC=mpicc to complie for h5utils. make all-am make[1]: Entering directory `/home/skkim/Download/h5utils-1.11.1' /usr/local/mpich/bin/mpicc -DHAVE_CONFIG_H -I. -I/usr/skkim/local/include -g -O2 -MT arrayh5.o -MD -MP -MF .deps/arrayh5.Tpo -c -o arrayh5.o arrayh5.c arrayh5.c:29:18: hdf5.h: No such file or directory arrayh5.c: In function `arrayh5_create_withdata': arrayh5.c:55: error: `stderr' undeclared (first use in this function) arrayh5.c:55: error: (Each undeclared identifier is reported only once arrayh5.c:55: error: for each function it appears in.) arrayh5.c: In function `arrayh5_transpose': arrayh5.c:137: error: `stderr' undeclared (first use in this function) arrayh5.c: In function `arrayh5_getrange': arrayh5.c:153: error: `stderr' undeclared (first use in this function) arrayh5.c: At top level: arrayh5.c:163: error: syntax error before find_dataset arrayh5.c:163: error: syntax error before group_id arrayh5.c: In function `find_dataset': arrayh5.c:165: error: `d' undeclared (first use in this function) arrayh5.c:166: error: `H5G_stat_t' undeclared (first use in this function) arrayh5.c:166: error: syntax error before info arrayh5.c:168: error: `group_id' undeclared (first use in this function) arrayh5.c:168: error: `name' undeclared (first use in this function) arrayh5.c:168: error: `info' undeclared (first use in this function) arrayh5.c:169: error: `H5G_DATASET' undeclared (first use in this function) arrayh5.c:170: error: `stderr' undeclared (first use in this function) Thanks in advance. S.K. Kim - Hi, I had a similar problem a couple of weeks ago with h5utils and parallel hdf5 libraries on my Mac. It can be fixed, or was fixed in my case, by adding this to the configure flags in addition to your other ones: CC=mpicc I think this tells the configure script/compiler to be expecting parallel libraries instead of serial ones. Hope this helps. Regards, Ian --- Research PhD Student Photonics Group Dept. of Electrical Electrical Engineering University of Bristol Rm 2.11, Queen's Building University Walk Bristol BS8 1TR ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
