Re: [Wien] error in dstart in Wine2k_16- "undefined symbol"
Dear Prof. Gavin Abo, I am very much grateful to you for your elaborate explanation of installing ifort variables. I did find /opt -name "libimf*" and it gave find: `/opt/test': Permission denied find: `/opt/intel/ism/lib': Permission denied So I tried to search the libimf.a manually (Before I used to run "locate libimf.a" and it gave nothing even I kept " source ..composer_xe_2015.5.223/bin/compilervars.sh intel64" in my .bashrc) and I found them at "../../composer_xe_2015.5.223/compilers/intel64/lib" and I placed this path to "$LD_LIBRARY_PATH in the .bashrc" . Now I re-compiled wien2k16 again and freshly did the initialization of the job. Now, I did not seen the error which I mentioned in my earlier mail and successfully completed the initialization process. thank you very much for your help venkatesh ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] error in dstart in Wine2k_16- "undefined symbol"
The libimf.a & libimf.so will not be were you installed WIEN2k. Those two files should be were the Intel Fortran compiler was installed, because they should come with the ifort program. If ifort was already installed by the manager(s) of your cluster (i.e., administrators, help desk team, or IT department) and is working on your cluster, you should not have to install Intel Fortran in your home directory on the cluster. However, if your cluster doesn't have ifort and you have to install ifort yourself in your home directory, I think you can just follow the instructions in Intel's Installation Guide for the version of the compiler that you have, where you should be able to get the Installation Guide from Intel. For example: https://software.intel.com/en-us/download/parallel-studio-xe-2017-install-guide-linux https://software.intel.com/en-us/download/parallel-studio-xe-2018-install-guide-linux At the first link above in parallel-studio-xe-install-guide-linux.pdf on page 8 in step 7.2., you should see: /Choose the installation directory (for example, /opt/intel)/ Instead of /opt/intel, you can change the installation directory to your home directory or another directory you have access to. Does the ifort command work when you login to the cluster? If it does not work, you will get a "command not found" error or something else like: username@computername:~$ ifort -v Command 'ifort' not found, did you mean: command 'isort' from deb isort Try: sudo apt install If the manager(s) installed ifort at the default location, it should be in the /opt folder. With ifort successfully installed, but getting the "command not found", what I do is search for and find the compilervars.sh: username@computername:~$ find /opt -name "compilervars.sh" /opt/intel/bin/compilervars.sh /opt/intel/composer_xe_2013_sp1.1.106/bin/compilervars.sh /opt/intel/composer_xe_2013_sp1/bin/compilervars.sh Then, I select the compilervars.sh for the version that I want to use among the versions available on the system. If the manager(s) of the cluster did not install ifort in the default /opt location, you will have contact them to find out where they installed it and replace the /opt in the above 'find' command with that location. From the above, I chose to use the general path one, which should use the latest ifort version on the system and appended the source line for it my .bashrc file: username@computername:~$ echo "source /opt/intel/bin/compilervars.sh intel64" >> ~/.bashrc I reload the .bashrc file with the source line change made to it: username@computername:~$ source ~/.bashrc If it does work, which it does on my system, I get the version number of the ifort compiler instead of the "command not found" error: username@computername:~$ ifort -v ifort version 14.0.1 If that already works, but I don't know where ifort is installed, I use the 'which' command: username@computername:~$ which ifort /opt/intel/composer_xe_2013_sp1.1.106/bin/intel64/ifort The above shows me it is installed in the /opt folder. When I search in the /opt folder, the libimf.a & libimf.so exist and are found: username@computername:~$ find /opt -name "libimf*" /opt/intel/composer_xe_2013_sp1.1.106/compiler/lib/mic/libimf.so /opt/intel/composer_xe_2013_sp1.1.106/compiler/lib/mic/libimf.a /opt/intel/composer_xe_2013_sp1.1.106/compiler/lib/intel64/libimf.so /opt/intel/composer_xe_2013_sp1.1.106/compiler/lib/intel64/libimf.a If the two files do not exist on the cluster, talk to your cluster manager(s) as maybe the Intel Fortran compiler needs to be reinstall by them. An alternative solution is possibly to compile WIEN2k statically using settings recommended by the Intel Link Advisor [ https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor ]. However, installing ifort and setting the environmental variable is most likely easier than trying to do a static build [ https://en.wikipedia.org/wiki/Static_build ]. thanks for your quick reply. I searched for libimf.a & libimf.so in the remote cluster where I was installed wine2k. But I could not found them. I already wrote the "source /path to compilevars.sh intel64" in .bashrc of my directory/user account. Now, I want to install myself libimf.a & libimf.so in my local directory. Could you please suggest me what I need to do. ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] error in dstart in Wine2k_16- "undefined symbol"
Dear Prof. Gavin Abo, thanks for your quick reply. I searched for libimf.a & libimf.so in the remote cluster where I was installed wine2k. But I could not found them. I already wrote the "source /path to compilevars.sh intel64" in .bashrc of my directory/user account. Now, I want to install myself libimf.a & libimf.so in my local directory. Could you please suggest me what I need to do. thanks venkatesh ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] error in dstart in Wine2k_16- "undefined symbol"
I believe the __libm_sse2_sincos symbol is defined in the files called libimf.a or libimf.so. If the Intel Fortran compiler is installed in the default location, then both of those files are usually in the /opt/intel/lib/intel64 directory on a 64 bit system. Do those two files exist on your system? The compilervars.sh script usually has to be executed so that the Linux environment can find those files. Did you have a source line for compilervars.sh in your .bashrc? If not, refer the Intel documentation at the following two links: https://software.intel.com/en-us/intel-system-studio-cplusplus-compiler-18.0-user-and-reference-guide-using-compilervars-file https://software.intel.com/en-us/articles/setting-up-the-build-environment-for-using-intel-c-or-fortran-compilers Also, you can check the mailing list archive [ https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/maillist.html ] for examples like: source replace_this_with_the_path_to_your_ifort_installation/compilervars.sh intel64 source /opt/intel/bin/compilervars.sh intel64 [ https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16702.html ] source /opt/ud/intel_xe_2016/parallel_studio_xe_2016.3.067/compilers_and_libraries_2016/linux/bin/compilervars.sh intel64 [ https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16590.html ] Though, on a cluster, you may want to first talk with your administrator before doing that, because it may be that they have some other procedure to set the environment for a WIEN2k calculation like a module load [ https://wiki.cse.ucdavis.edu/support/hpc/software/wien2k ]. On 6/6/2018 9:07 AM, venkatesh chandragiri wrote: Dear wien2k users, I have successfully complied Wine2k_16 and start to run init_lapw for the MnSb compound. Up to kgen it was successfully done. But for dstart it shows error as given below. === next is dstart > dstart -c -p (22:46:57) running dstart in single mode dstart: symbol lookup error: dstart: *undefined symbol: __libm_sse2_sincos* 0.015u 0.009s 0:00.06 16.6% 0+0k 0+0io 0pf+0w error: command /share/home/venky/soft/wien2k/dstartpara -c dstart.def failed n stop error n [venky@mgt02 MnSb]$ x dstart /share/home/venky/soft/wien2k/dstart: *symbol lookup error: */share/home/venky/soft/wien2k/dstart: *undefined symbol: __libm_sse2_sincos* 0.002u 0.002s 0:00.00 0.0% 0+0k 0+0io 0pf+0w error: command /share/home/venky/soft/wien2k/dstart dstart.def failed This problem was not seen the wien2k_13 which was installed in the other server previously. kindly guide me to rectify this error. thanks venkatesh ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] error in dstart in Wine2k_16- "undefined symbol"
Dear wien2k users, I have successfully complied Wine2k_16 and start to run init_lapw for the MnSb compound. Up to kgen it was successfully done. But for dstart it shows error as given below. === next is dstart > dstart -c -p(22:46:57) running dstart in single mode dstart: symbol lookup error: dstart: *undefined symbol: __libm_sse2_sincos* 0.015u 0.009s 0:00.06 16.6% 0+0k 0+0io 0pf+0w error: command /share/home/venky/soft/wien2k/dstartpara -c dstart.def failed n stop error n [venky@mgt02 MnSb]$ x dstart /share/home/venky/soft/wien2k/dstart: *symbol lookup error: */share/home/venky/soft/wien2k/dstart: *undefined symbol: __libm_sse2_sincos* 0.002u 0.002s 0:00.00 0.0% 0+0k 0+0io 0pf+0w error: command /share/home/venky/soft/wien2k/dstart dstart.def failed This problem was not seen the wien2k_13 which was installed in the other server previously. kindly guide me to rectify this error. thanks venkatesh ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
