July 2013 - Comp-phys-alps-users

Re: [ALPS-users] Building ALPS on Ubuntu 12.04 - error when building TEBD
by Joseph Prentice 22 Jul '13

22 Jul '13

Hi all, sorry to send a second email, but don't worry, a colleague has helped me out. We've fixed it by writing the full path to the dmrg (or other applications) file for everything other than TEBD. For TEBD, we had to edit the tools.py file, in the runTEBD function, inserting the full path to the tebd file. Thanks for all your help, Joseph Prentice ________________________________________ From: comp-phys-alps-users-bounces(a)lists.phys.ethz.ch [comp-phys-alps-users-bounces(a)lists.phys.ethz.ch] on behalf of comp-phys-alps-users-request(a)lists.phys.ethz.ch [comp-phys-alps-users-request(a)lists.phys.ethz.ch] Sent: 22 July 2013 11:00 To: comp-phys-alps-users(a)lists.phys.ethz.ch Subject: Comp-phys-alps-users Digest, Vol 88, Issue 6 Send Comp-phys-alps-users mailing list submissions to comp-phys-alps-users(a)lists.phys.ethz.ch To subscribe or unsubscribe via the World Wide Web, visit https://lists.phys.ethz.ch/listinfo/comp-phys-alps-users or, via email, send a message with subject or body 'help' to comp-phys-alps-users-request(a)lists.phys.ethz.ch You can reach the person managing the list at comp-phys-alps-users-owner(a)lists.phys.ethz.ch When replying, please edit your Subject line so it is more specific than "Re: Contents of Comp-phys-alps-users digest..." Today's Topics: 1. Re: Building ALPS on Ubuntu 12.04 - error when building TEBD (Matthias Troyer) ---------------------------------------------------------------------- Message: 1 Date: Sun, 21 Jul 2013 15:34:32 -0600 From: Matthias Troyer <troyer(a)phys.ethz.ch> To: comp-phys-alps-users(a)lists.phys.ethz.ch Subject: Re: [ALPS-users] Building ALPS on Ubuntu 12.04 - error when building TEBD Message-ID: <EEF93DDC-244A-47D3-89D5-5AA60BCBC0AD(a)phys.ethz.ch> Content-Type: text/plain; charset="us-ascii" Hi Joesph, You will need to add -fopenmp to your Fortran compilation flags Best regards Matthias On Jul 18, 2013, at 9:51 AM, Joseph Prentice <Joseph.Prentice(a)physics.ox.ac.uk> wrote: > Hi all, > > Apologies for changing tack, given my previous message about installing on Mac OS X 10.7.5, but I have instead tried installing ALPS on Ubuntu 12.04, following the instructions on the wiki, with admin privileges now. After getting the dependent libraries as described, to compile ALPS I initially used the command: > $ sudo cmake -DALPS_BUILD_FORTRAN=ON -DCMAKE_INSTALL_PREFIX=/home/prentice/Documents/ALPSInstall/ /home/prentice/Documents/ALPS/alps-2.1.1-r6176-src/alps > and this seemed to work well. I then used sudo make and let ALPS build. However, at about 64% in, I got the following message: > Scanning dependencies of target tebd > [ 62%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/GlobalData.f90.o > [ 62%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/LinearOps.f90.o > [ 62%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/HamiOps.f90.o > [ 63%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/StateOps.f90.o > [ 63%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/LocalOps.f90.o > [ 63%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/ObOps.f90.o > [ 63%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/Hdf5Interface.f90.o > [ 64%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/PropOps.f90.o > [ 64%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/tebd.f90.o > Linking Fortran executable tebd > CMakeFiles/tebd.dir/tebd.f90.o: In function `MAIN__': > tebd.f90:(.text+0x8b0): undefined reference to `omp_get_num_procs_' > tebd.f90:(.text+0x9ab): undefined reference to `omp_set_num_threads_' > collect2: ld returned 1 exit status > make[2]: *** [applications/dmrg/tebd/tebd] Error 1 > make[1]: *** [applications/dmrg/tebd/CMakeFiles/tebd.dir/all] Error 2 > make: *** [all] Error 2 > > Are there any ideas about what can be done with this? There doesn't appear to be a problem with OpenMP, as we have tested it with another simple program, and I have Googled the error too, with no results. I am stumped, and any help would be greatly appreciated. I will attach the CMakeCache.txt file if that is of use. > > Thank you very much, > Joseph Prentice > <TEBD Fail Ubuntu CMakeCache.txt.gz>

1 0

Re: [ALPS-users] Building ALPS on Ubuntu 12.04 - error when building TEBD
by Joseph Prentice 22 Jul '13

22 Jul '13

Thank you very much Michele and Matthias! I turned on the ALPS_ENABLE_OPENMP option and I've managed to install without any problems. However, I now have the problem that whenever I try to run one of the tutorial Python scripts, by running: sudo /home/prentice/Documents/ALPSInstall/bin/alpspython ~/Documents/ALPSInstall/tutorials/dmrg-01-dmrg/spin_one_half.py I get the error message: /bin/sh: 1: dmrg: not found Traceback (most recent call last): File "/home/prentice/Documents/ALPSInstall/tutorials/dmrg-01-dmrg/spin_one_half.py", line 51, in <module> data = pyalps.loadEigenstateMeasurements(pyalps.getResultFiles(prefix='parm_spin_one_half')) File "/home/prentice/Documents/ALPSInstall/lib/pyalps/tools.py", line 397, in getResultFiles res=recursiveGlob(dirname, pattern) File "/home/prentice/Documents/ALPSInstall/lib/pyalps/tools.py", line 374, in recursiveGlob ret += recursiveGlob(os.path.join(dirname, d), pattern) File "/home/prentice/Documents/ALPSInstall/lib/pyalps/tools.py", line 374, in recursiveGlob ret += recursiveGlob(os.path.join(dirname, d), pattern) File "/home/prentice/Documents/ALPSInstall/lib/pyalps/tools.py", line 372, in recursiveGlob for d in os.listdir(dirname): OSError: [Errno 20] Not a directory: './dev/cdrom' The key problem, I thought, was that dmrg cannot be found, and I'm not sure how to fix this. I've gone back through the archives here and tried editing the .bashrc file, which fixed a similar problem, but didn't work for me. Any ideas how I can fix this? It's a problem with all the tutorials, TEBD, MC, etc. Thank you again, Joseph On 22 Jul 2013, at 11:00, <comp-phys-alps-users-request(a)lists.phys.ethz.ch<mailto:comp-phys-alps-users-request@lists.phys.ethz.ch>> wrote: Send Comp-phys-alps-users mailing list submissions to comp-phys-alps-users(a)lists.phys.ethz.ch<mailto:comp-phys-alps-users@lists.phys.ethz.ch> To subscribe or unsubscribe via the World Wide Web, visit https://lists.phys.ethz.ch/listinfo/comp-phys-alps-users or, via email, send a message with subject or body 'help' to comp-phys-alps-users-request(a)lists.phys.ethz.ch You can reach the person managing the list at comp-phys-alps-users-owner(a)lists.phys.ethz.ch When replying, please edit your Subject line so it is more specific than "Re: Contents of Comp-phys-alps-users digest..." Today's Topics: 1. Re: Building ALPS on Ubuntu 12.04 - error when building TEBD (Matthias Troyer) ---------------------------------------------------------------------- Message: 1 Date: Sun, 21 Jul 2013 15:34:32 -0600 From: Matthias Troyer <troyer(a)phys.ethz.ch> To: comp-phys-alps-users(a)lists.phys.ethz.ch Subject: Re: [ALPS-users] Building ALPS on Ubuntu 12.04 - error when building TEBD Message-ID: <EEF93DDC-244A-47D3-89D5-5AA60BCBC0AD(a)phys.ethz.ch> Content-Type: text/plain; charset="us-ascii" Hi Joesph, You will need to add -fopenmp to your Fortran compilation flags Best regards Matthias On Jul 18, 2013, at 9:51 AM, Joseph Prentice <Joseph.Prentice(a)physics.ox.ac.uk> wrote: Hi all, Apologies for changing tack, given my previous message about installing on Mac OS X 10.7.5, but I have instead tried installing ALPS on Ubuntu 12.04, following the instructions on the wiki, with admin privileges now. After getting the dependent libraries as described, to compile ALPS I initially used the command: $ sudo cmake -DALPS_BUILD_FORTRAN=ON -DCMAKE_INSTALL_PREFIX=/home/prentice/Documents/ALPSInstall/ /home/prentice/Documents/ALPS/alps-2.1.1-r6176-src/alps and this seemed to work well. I then used sudo make and let ALPS build. However, at about 64% in, I got the following message: Scanning dependencies of target tebd [ 62%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/GlobalData.f90.o [ 62%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/LinearOps.f90.o [ 62%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/HamiOps.f90.o [ 63%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/StateOps.f90.o [ 63%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/LocalOps.f90.o [ 63%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/ObOps.f90.o [ 63%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/Hdf5Interface.f90.o [ 64%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/PropOps.f90.o [ 64%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/tebd.f90.o Linking Fortran executable tebd CMakeFiles/tebd.dir/tebd.f90.o: In function `MAIN__': tebd.f90:(.text+0x8b0): undefined reference to `omp_get_num_procs_' tebd.f90:(.text+0x9ab): undefined reference to `omp_set_num_threads_' collect2: ld returned 1 exit status make[2]: *** [applications/dmrg/tebd/tebd] Error 1 make[1]: *** [applications/dmrg/tebd/CMakeFiles/tebd.dir/all] Error 2 make: *** [all] Error 2 Are there any ideas about what can be done with this? There doesn't appear to be a problem with OpenMP, as we have tested it with another simple program, and I have Googled the error too, with no results. I am stumped, and any help would be greatly appreciated. I will attach the CMakeCache.txt file if that is of use. Thank you very much, Joseph Prentice <TEBD Fail Ubuntu CMakeCache.txt.gz>

2 2

Building ALPS on Ubuntu 12.04 - error when building TEBD
by Joseph Prentice 21 Jul '13

21 Jul '13

Hi all, Apologies for changing tack, given my previous message about installing on Mac OS X 10.7.5, but I have instead tried installing ALPS on Ubuntu 12.04, following the instructions on the wiki, with admin privileges now. After getting the dependent libraries as described, to compile ALPS I initially used the command: $ sudo cmake -DALPS_BUILD_FORTRAN=ON -DCMAKE_INSTALL_PREFIX=/home/prentice/Documents/ALPSInstall/ /home/prentice/Documents/ALPS/alps-2.1.1-r6176-src/alps and this seemed to work well. I then used sudo make and let ALPS build. However, at about 64% in, I got the following message: Scanning dependencies of target tebd [ 62%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/GlobalData.f90.o [ 62%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/LinearOps.f90.o [ 62%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/HamiOps.f90.o [ 63%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/StateOps.f90.o [ 63%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/LocalOps.f90.o [ 63%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/ObOps.f90.o [ 63%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/Hdf5Interface.f90.o [ 64%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/core/PropOps.f90.o [ 64%] Building Fortran object applications/dmrg/tebd/CMakeFiles/tebd.dir/tebd.f90.o Linking Fortran executable tebd CMakeFiles/tebd.dir/tebd.f90.o: In function `MAIN__': tebd.f90:(.text+0x8b0): undefined reference to `omp_get_num_procs_' tebd.f90:(.text+0x9ab): undefined reference to `omp_set_num_threads_' collect2: ld returned 1 exit status make[2]: *** [applications/dmrg/tebd/tebd] Error 1 make[1]: *** [applications/dmrg/tebd/CMakeFiles/tebd.dir/all] Error 2 make: *** [all] Error 2 Are there any ideas about what can be done with this? There doesn't appear to be a problem with OpenMP, as we have tested it with another simple program, and I have Googled the error too, with no results. I am stumped, and any help would be greatly appreciated. I will attach the CMakeCache.txt file if that is of use. Thank you very much, Joseph Prentice

3 2

Re: [ALPS-users] TEBD will not be built when building ALPS on Mac OS X 10.7.5
by Joseph Prentice 17 Jul '13

17 Jul '13

I believe this is the right file. I haven't explicitly specified a Fortran compiler, but the default one that is being used is 4.5. After looking at it some more, I believe that there might be something wrong between the ALPS code and the version of CMake I am using (which is the one within MacPorts, 2.8.10), as some variables have been changed I understand? On 14 Jul 2013, at 11:00, <comp-phys-alps-users-request(a)lists.phys.ethz.ch> <comp-phys-alps-users-request(a)lists.phys.ethz.ch> wrote: > Send Comp-phys-alps-users mailing list submissions to > comp-phys-alps-users(a)lists.phys.ethz.ch > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.phys.ethz.ch/listinfo/comp-phys-alps-users > or, via email, send a message with subject or body 'help' to > comp-phys-alps-users-request(a)lists.phys.ethz.ch > > You can reach the person managing the list at > comp-phys-alps-users-owner(a)lists.phys.ethz.ch > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Comp-phys-alps-users digest..." > > > Today's Topics: > > 1. TEBD will not be built when building ALPS on Mac OS X 10.7.5 > (Joseph Prentice) > 2. Re: TEBD will not be built when building ALPS on Mac OS X > 10.7.5 (Matthias Troyer) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 13 Jul 2013 10:54:15 +0000 > From: Joseph Prentice <Joseph.Prentice(a)physics.ox.ac.uk> > To: "comp-phys-alps-users(a)lists.phys.ethz.ch" > <comp-phys-alps-users(a)lists.phys.ethz.ch> > Subject: [ALPS-users] TEBD will not be built when building ALPS on Mac > OS X 10.7.5 > Message-ID: > <747861816F6A5C47BE50FCA07F5B2B4A0D3A90(a)EXCHNG16.physics.ox.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > Hi everyone, > I've been trying to install ALPS in order to use TEBD on Mac OS X 10.7.5, by building it from source. I've also been using MacPorts in order to get the dependent libraries. Using MacPorts, I have installed the ports (and variants) 'cmake +gui' and 'hdf5-18 +fortran +openmpi', and I have directly downloaded ALPS and Boost 1.50.0, following the instructions on the 'Building ALPS from source' page on the ALPS wiki. However, when I try to run the command: > > cmake -DCMAKE_INSTALL_PREFIX=/Volumes/Scratch/Build_Directory /home/prentice/Downloads/alps-2.1.1-r6176-src-with-boost/alps > > (which I use because I am not an administrator on my Mac, so I don't have writing privileges), ALPS seems to build, but I get the message 'tebd will not be built'. Can anyone give me some help on how to fix this? I'm very new to pretty much everything I'm using here, so any help would be much appreciated. > > I'll attach the full text from the Terminal. > > Thanks, > Joseph Prentice >

2 1

TEBD will not be built when building ALPS on Mac OS X 10.7.5
by Joseph Prentice 13 Jul '13

13 Jul '13

Hi everyone, I've been trying to install ALPS in order to use TEBD on Mac OS X 10.7.5, by building it from source. I've also been using MacPorts in order to get the dependent libraries. Using MacPorts, I have installed the ports (and variants) 'cmake +gui' and 'hdf5-18 +fortran +openmpi', and I have directly downloaded ALPS and Boost 1.50.0, following the instructions on the 'Building ALPS from source' page on the ALPS wiki. However, when I try to run the command: cmake -DCMAKE_INSTALL_PREFIX=/Volumes/Scratch/Build_Directory /home/prentice/Downloads/alps-2.1.1-r6176-src-with-boost/alps (which I use because I am not an administrator on my Mac, so I don't have writing privileges), ALPS seems to build, but I get the message 'tebd will not be built'. Can anyone give me some help on how to fix this? I'm very new to pretty much everything I'm using here, so any help would be much appreciated. I'll attach the full text from the Terminal. Thanks, Joseph Prentice

2 1

Problem in installing Alps and vistrail
by Soumen Bag 05 Jul '13

05 Jul '13

Dear Sir, I have installed apls 2.2.1-win 64 and visrail 2.0- win32 But this can link to alps, Mc-1 executed properly.. problem is that it cant execute DMFT-02 Hybridization This problem may be because of following problem shown during installation of vistrail. ------------------------------------------------------------------------------- CRITICAL 2013-07-04 17:24:37,227 C:\Program Files (x86)\VisTrails\vistrails\core\packagemanager.py, line 534 Package initialization failed <codepath rpy> CRITICAL 2013-07-04 17:24:37,262 C:\Program Files (x86)\VisTrails\vistrails\core\packagemanager.py, line 535 Will disable package <codepath rpy> CRITICAL 2013-07-04 17:24:37,263 C:\Program Files (x86)\VisTrails\vistrails\core\packagemanager.py, line 536 Package 'R' failed to initialize, raising 'ImportError: No module named rpy2.robjects'. Traceback: Traceback (most recent call last): File "C:\Program Files (x86)\VisTrails\vistrails\core\modules\module_registry.py", line 1414, in initialize_package package.initialize() File "C:\Program Files (x86)\VisTrails\vistrails\core\modules\package.py", line 369, in initialize __import__(name, globals(), locals(), []) File "C:\Program Files (x86)\VisTrails\vistrails\core\modules\package.py", line 263, in _import (name, globals, locals, fromlist, level)) File "C:\Program Files (x86)\VisTrails\vistrails\packages\rpy\init.py", line 42, in <module> import rpy2.robjects as robjects File "C:\Program Files (x86)\VisTrails\vistrails\core\modules\package.py", line 263, in _import (name, globals, locals, fromlist, level)) ImportError: No module named rpy2.robjects CRITICAL 2013-07-04 17:24:51,118 C:\Program Files (x86)\VisTrails\vistrails\core\bundles\pyimport.py, line 63 Package installation failed. CRITICAL 2013-07-04 17:24:51,119 C:\Program Files (x86)\VisTrails\vistrails\core\bundles\pyimport.py, line 64 Package might not be available in the provided repositories. CRITICAL 2013-07-04 17:24:51,121 C:\Program Files (x86)\VisTrails\vistrails\core\packagemanager.py, line 534 Package initialization failed <codepath sql> CRITICAL 2013-07-04 17:24:51,122 C:\Program Files (x86)\VisTrails\vistrails\core\packagemanager.py, line 535 Will disable package <codepath sql> CRITICAL 2013-07-04 17:24:51,128 C:\Program Files (x86)\VisTrails\vistrails\core\packagemanager.py, line 536 Package 'SQL' failed to initialize, raising 'ImportError: No module named MySQLdb'. Traceback: Traceback (most recent call last): File "C:\Program Files (x86)\VisTrails\vistrails\core\modules\module_registry.py", line 1414, in initialize_package package.initialize() File "C:\Program Files (x86)\VisTrails\vistrails\core\modules\package.py", line 369, in initialize __import__(name, globals(), locals(), []) File "C:\Program Files (x86)\VisTrails\vistrails\core\modules\package.py", line 263, in _import (name, globals, locals, fromlist, level)) File "C:\Program Files (x86)\VisTrails\vistrails\packages\sql\init.py", line 38, in <module> 'linux-fedora':'MySQL-python'}) File "C:\Program Files (x86)\VisTrails\vistrails\core\bundles\pyimport.py", line 65, in py_import raise e ImportError: No module named MySQLdb -------------------------------------------------------------------- Previously i tried with Alps- Win-64 and Vistrail-win-64 but at that combination vistrail cant enable Alps modules (Same kind of error was shown) Thanking You, *Soumen Kumar Bag* *Physical Science Dept.* *IISC*

2 1