Dear Nick, The Suse liux is not available at the monment. But a Red Hat linux is the same case. the lowercase and uppercase work.
For these, I use the same ifort, mkl. Best regards. Guangping Zhang 2013-10-10 发件人：Nick Papior Andersen <[email protected]> 发送时间：2013-10-10 11:29 主题：Re: [SIESTA-L] Bus error during Transiesta in trunk428 收件人："[email protected]"<[email protected]> 抄送： Yeah, that is strange... It should at least be consistent if your compilers, libaries etc. are the same (however SUSE and Ubuntu don't share library repos... so...). Nevermind, keep them lowercase for the future... :) That should be portable, it did work by having lower case on SUSE right? Kind regards Nick 2013/10/10 zgp121 <[email protected]> Dear Nick, Thanks for your advices. Yes. I am sure. On the suse cluster, it did work for "Variables". When I transfer this fdf file to Ubuntu, this file does not work. I thought it was due to the compiling. So I recompiling the transiesta executable again and again, it still failed. Finally I found the reasion. The attachment is one of the output file on the suse linux. You can see it clearly. But the same file does not work on the Ubuntu any more. Thanks very much. Yours, Guangping Zhang 2013-10-10 发件人：Nick Papior Andersen <[email protected]> 发送时间：2013-10-10 11:11 主题：Re: [SIESTA-L] Bus error during Transiesta in trunk428 收件人："[email protected]"<[email protected]> 抄送： Transferring binary files across different architectures is highly inadvisable! And will almost definitely fail. So do try to avoid this. That part of the fdf is actually case-sensitive as it searches by the fortran INDEX routine which matches case. It should be case sensitive on both of them for the z-matrix blocks, i.e. these should be lower-case: molecule scale, frac, cart constant variable constraint Are you sure you they behave differently? Kind regards Nick 2013/10/10 zgp121 <[email protected]> Dear Nick, Thanks for your quick reply. I have make a sample of k-points on the electrode. But the TSHS file of electrode is calcualted on anothter cluster of which the OS is Suse. Due to the memeory capacity, I have to use a large memeory cluster. But on this one, the OS is Ubuntu. So I guess, the error may be caused by this. So I recalculate the electrode on the new cluster. The task is in the queue. I hope this can solve this problem. If it does not work, I will follow your instruction step by step to figure out the reasion. But another thing strange I have met is: in the mannul it saids the fdf is case insensitive. And this is true in the suse cluster. But on the Ubuntu cluster, it not the case. In Z-matrix declaration, the key word "Variables" is not recognized, it must be "variables". Is this because Ubuntu? Best regard. Yours Guangping Zhang 2013-10-10 发件人：Nick Papior Andersen <[email protected]> 发送时间：2013-10-10 08:48 主题：Re: [SIESTA-L] Bus error during Transiesta in trunk428 收件人："[email protected]"<[email protected]> 抄送： The only deallocation performed by node 0 is an array containing the atomic species, I suspect you see the same error no matter the number of cores used? It could mean a couple of things, the electrode TSHS is not fully populated (i.e. erroneous), you did a Gamma-point electrode calculation, or that there is an actual error in the communication. Can you please supply your electrode and transiesta fdf files. Could you please try and goto line 1055 of file Src/m_ts_electrode.F90 and add this (right before the "call memory" line): print*,allocated(isa),isa and recompile/run and return the output to me? Kind regards Nick 2013/10/10 zgp121 <[email protected]> Dear SIESTA users: When I use 24 cores to run the TranSIESTA calculation using trunk 428, I got the error like this: /var/spool/slurmd/job1321828/slurm_script: line 12: 19218 Bus error mpirun transiesta < trans-0.0.fdf > trans-0.0.log And I also find the following message in trans-0.0.log: Creating Green's function file for: left WARNING: alloc-realloc-dealloc name mismatch Name: elec_HS unknown Size: -588. Bytes Node: 0 Subsequent mismatches will not be reported The system of the HPC is Ubuntu. And in the compiliation, Ifort(10.1.012), MKL(10.0.2.018), OpenMPI(1.4.5) are used. Can anyone figure out what is the problem? Guangping Zhang 2013-10-10
