[Wien] libstdc++.so.5

Tue Sep 28 09:09:23 CEST 2010

Dear WIEN2k members,

I am trying to compile the latest version of the code using FC10 (Intel ifort 11.1 compiler + mkl) on an isolated 64 bit intel 4 cores system and an isolated 32 bit intel 2 cores system. 
For the 32 bit system I do not have any problem even under FC11, FC12, and FC13, and the code works fine. But for the former 64 bit system there is the following error in compile.msg files:

"/opt/intel/Compiler/11.1/072/bin/intel64/fortcom: error while loading shared libraries: libstdc++.so.5: cannot open shared object file: No such file or directory"

This is in the case that I have already installed the libstdc++.so.5 library, as it is also necessary for installing the intel ifort 11.1 compiler.

Although in FC10 the libstdc++.so.6 is installed, the libstdc++.so.5 is also needed for installing intel ifort 11.1 compiler. Therefore, I installed the later library and all of its components using yum as "yum install libstdc++.so.5". After this the l_cprof_p_11.1.072 is completely and successfully installed. I added the following two lines in .bashrc:
source /opt/intel/Compiler/11.1/072/mkl/tools/environment/mklvars64.sh
source /opt/intel/Compiler/11.1/072/bin/intel64/ifortvars_intel64.sh
Then siteconfig_lapw recognized ifort and mkl.

The libstdc++.so.5 is installed in /usr/lib in the 32 bit system, where the libstdc++.so.6 was installed.
The libstdc++.so.5 is installed in /usr/lib in the 64 bit system, while the libstdc++.so.6 was installed in another directory of /usr/lib64.

In the directory of /usr/lib on the 32 bit system there are:
#find -name "libsdtc*"
./gcc/x86_64-redhat-linux/4.4.4/libstdc++.so
./gcc/x86_64-redhat-linux/4.4.4/32/libstdc++.so
./gcc/x86_64-redhat-linux/4.4.4/32/libstdc++.a
./gcc/x86_64-redhat-linux/4.4.4/libstdc++.a
./libstdc++.so.5.0.7
./libstdc++.so.5

In the directory of /usr/lib on the 64 bit system there are:
#find -name "libsdtc*"
./gcc/x86_64-redhat-linux/4.3.2/libstdc++.a
./gcc/x86_64-redhat-linux/4.3.2/32/libstdc++.a
./gcc/x86_64-redhat-linux/4.3.2/32/libstdc++.so
./gcc/x86_64-redhat-linux/4.3.2/libstdc++.so
./libstdc++.so.5.0.7
./libstdc++.so.5

In the directory of /usr/lib64 on the 64 bit system there are:
#find -name "libsdtc*"
./libstdc++.so.6.0.10
./libstdc++.so.6

For the 64 bit system, I added the /usr/lib path to the $PATH, but still the problem exists. 

Any reply is highly appreciated.

Sincerely yours,
S. Jalali
/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
Saeid Jalali Asadabadi,
Department of Physics, Faculty of Science,
University of Isfahan (UI), Hezar Gerib Avenue,
81744 Isfahan, Iran.
Phones:
Dep. of Phys.  :+98-0311-793 2435
Office         :+98-0311-793 4176
Fax No.        :+98-0311-793 2409
E-mail         :sjalali at phys.ui.ac.ir
Homepage       :http://sci.ui.ac.ir/~sjalali
www            :http://www.ui.ac.ir
/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
>-----Original Message-----
>From: wien-bounces at zeus.theochem.tuwien.ac.at [mailto:wien-
>bounces at zeus.theochem.tuwien.ac.at] On Behalf Of Laurence Marks
>Sent: Sunday, September 26, 2010 5:41 PM
>To: A Mailing list for WIEN2k users
>Subject: *** SPAM *** [5.7] Re: [Wien] Slab convergence -- continuation
>
>An additional comment/question -- did you use the default spin setting
>in instgen_lapw? I wonder if you did, and that in the converged
>density the Au is mainly non-polarized except slightly at the surface.
>However, you started it with all the Au polarized and it will take
>many iterations for the spin to come down to close to the correct
>value, and only then will it converge.
>
>If I am right, you can look at this in case.scfm (or case.scf) and,
>next time, edit your case.inst by hand or use the option that allows
>you to specify for each atom. Starting closer to the right spin
>coupled with using a centro-symmetric cell will probably solve your
>problems.
>
>On Sat, Sep 25, 2010 at 5:33 PM, Laurence Marks
><L-marks at northwestern.edu> wrote:
>> There is nothing wrong, it is converging slowly and my guess is that
>> it will need 60-80 iterations as you currently have it modelled. If
>> you have only run it for 20 iterations, do another 20 and use the -NI
>> option so it keeps going. DO NOT RESTART from dstart.
>>
>> N.B., the forces are not meaningful unless you have "FOR" instead of
>> "TOT" and the densities are much better converged than this.
>>
>> On Sat, Sep 25, 2010 at 5:14 PM, Lukasz Plucinski
>> <pluto at physics.ucdavis.edu> wrote:
>>> �Dear Laurence, Prof. Blaha,
>>>
>>> 19 iterations with settings suggested by Prof. Blaha have passed
>(still with
>>> complex version of the program), but I guess there are no signs of
>>> convergence. I will keep working on this, and I am sure it will work
>at the
>>> end, especially that I made big progress already :) Next step would
>be to
>>> run smaller slab, like Fe1Au10, and try the non-complex version.
>>>
>>> In any case I decided to paste the output of the grep file you have
>proposed
>>> - maybe you will immediately see some obvious problem (Fe is atom 21
>and it
>>> connects to Au atom 1). At the end I also print the forces for the
>last
>>> iteration and forces for Fe atom over the 19 iterations - maybe those
>are
>>> too high...
>>>
>>> lplucin at iff187:Fe1Au20% grep -e :DIR -e GREED -e :FRMS -e :ENE -e
>:CHARG -e
>>> PRATT -e :DIS -e "MIXING SC" -e PLANE *.scf $1
>>> :DIS �: �CHARGE DISTANCE � � � ( 1.8369011 for atom � 21 spin 2)
>>> �0.7633234
>>> :PLANE: �INTERSTITIAL TOTAL � �118.34106 DISTAN �0.118D+01 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.39867 DISTAN �0.136D+01 %
>>> � � � PRATT MIXING SCHEME WITH 0.025
>>> :ENE �: ********** TOTAL ENERGY IN Ry = � � �-764461.70817746
>>> :DIS �: �CHARGE DISTANCE � � � ( 3.4564629 for atom � �1 spin 2)
>>> �1.8459239
>>> :PLANE: �INTERSTITIAL TOTAL � �115.72078 DISTAN �0.110D+01 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.39736 DISTAN �0.376D+01 %
>>> :DIRM : �MEMORY 1/8 RESCALE �2.905 RED �2.494 PRED �1.000 NEXT �0.367
>>> :DIRP : �|BROYD|= 0.747D-01 |PRATT|= 0.155D+00 ANGLE= 163.0 DEGREES
>>> :DIRB : �|BROYD|= 0.254D+00 |PRATT|= 0.921D+00 ANGLE= �55.5 DEGREES
>>> � � � MSEC1 MIXING SCHEME WITH 0.015
>>> :ENE �: *WARNING** TOTAL ENERGY IN Ry = � � �-764479.28101496
>>> :DIS �: �CHARGE DISTANCE � � � ( 1.9111839 for atom � 21 spin 2)
>>> �0.9887058
>>> :PLANE: �INTERSTITIAL TOTAL � �116.39701 DISTAN �0.116D+01 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.39749 DISTAN �0.173D+01 %
>>> :DIRM : �MEMORY 2/8 RESCALE �2.838 RED �0.487 PRED �0.367 NEXT �0.748
>>> :DIRP : �|BROYD|= 0.183D+00 |PRATT|= 0.321D+00 ANGLE= � 3.9 DEGREES
>>> :DIRB : �|BROYD|= 0.378D+00 |PRATT|= 0.896D+00 ANGLE= �38.8 DEGREES
>>> � � � MSEC1 MIXING SCHEME WITH 0.030
>>> :ENE �: ********** TOTAL ENERGY IN Ry = � � �-764463.27396102
>>> :DIS �: �CHARGE DISTANCE � � � ( 2.0879620 for atom � 21 spin 2)
>>> �1.1862428
>>> :PLANE: �INTERSTITIAL TOTAL � �114.65422 DISTAN �0.115D+01 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.39637 DISTAN �0.200D+01 %
>>> :DIRM : �MEMORY 3/8 RESCALE �2.865 RED �1.133 PRED �0.748 NEXT �0.661
>>> :DIRP : �|BROYD|= 0.313D-01 |PRATT|= 0.280D+00 ANGLE= 172.8 DEGREES
>>> :DIRB : �|BROYD|= 0.639D-01 |PRATT|= 0.897D+00 ANGLE= 124.3 DEGREES
>>> � � � MSEC1 MIXING SCHEME WITH 0.026
>>> :ENE �: ********** TOTAL ENERGY IN Ry = � � �-764465.27438637
>>> :DIS �: �CHARGE DISTANCE � � � ( 1.9582611 for atom � 21 spin 2)
>>> �1.0047914
>>> :PLANE: �INTERSTITIAL TOTAL � �114.94778 DISTAN �0.116D+01 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.39654 DISTAN �0.172D+01 %
>>> :DIRM : �MEMORY 4/8 RESCALE �2.835 RED �0.874 PRED �0.661 NEXT �0.648
>>> :DIRP : �|BROYD|= 0.637D+00 |PRATT|= 0.320D+00 ANGLE= � 4.9 DEGREES
>>> :DIRB : �|BROYD|= 0.121D+01 |PRATT|= 0.896D+00 ANGLE= �39.2 DEGREES
>>> � � � MSEC1 MIXING SCHEME WITH 0.030
>>> :ENE �: ********** TOTAL ENERGY IN Ry = � � �-764463.63839698
>>> :DIS �: �CHARGE DISTANCE � � � ( 2.3237103 for atom � 21 spin 2)
>>> �1.7790288
>>> :PLANE: �INTERSTITIAL TOTAL � �108.90635 DISTAN �0.114D+01 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.39379 DISTAN �0.297D+01 %
>>> :DIRM : �MEMORY 5/8 RESCALE �2.939 RED �1.644 PRED �0.648 NEXT �0.385
>>> :DIRP : �|BROYD|= 0.488D-02 |PRATT|= 0.188D+00 ANGLE= �86.6 DEGREES
>>> :DIRB : �|BROYD|= 0.870D-01 |PRATT|= 0.900D+00 ANGLE= �53.0 DEGREES
>>> � � � MSEC1 MIXING SCHEME WITH 0.018
>>> :ENE �: *WARNING** TOTAL ENERGY IN Ry = � � �-764472.65423111
>>> :DIS �: �CHARGE DISTANCE � � � ( 0.6292669 for atom � �2 spin 2)
>>> �0.7338108
>>> :PLANE: �INTERSTITIAL TOTAL � �108.91944 DISTAN �0.115D+01 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.39367 DISTAN �0.962D+00 %
>>> :DIRM : �MEMORY 6/8 RESCALE �2.760 RED �0.375 PRED �0.385 NEXT �0.785
>>> :DIRP : �|BROYD|= 0.304D+00 |PRATT|= 0.356D+00 ANGLE= � 3.3 DEGREES
>>> :DIRB : �|BROYD|= 0.453D+00 |PRATT|= 0.673D+00 ANGLE= �35.6 DEGREES
>>> � � � MSEC1 MIXING SCHEME WITH 0.037
>>> :ENE �: ********** TOTAL ENERGY IN Ry = � � �-764462.68273654
>>> :DIS �: �CHARGE DISTANCE � � � ( 1.4736987 for atom � 21 spin 2)
>>> �0.7422774
>>> :PLANE: �INTERSTITIAL TOTAL � �106.01865 DISTAN �0.113D+01 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.39239 DISTAN �0.215D+01 %
>>> :DIRM : �MEMORY 7/8 RESCALE �2.806 RED �1.952 PRED �0.785 NEXT �0.410
>>> :DIRP : �|BROYD|= 0.290D+00 |PRATT|= 0.178D+00 ANGLE= 175.8 DEGREES
>>> :DIRB : �|BROYD|= 0.438D+00 |PRATT|= 0.676D+00 ANGLE= 110.2 DEGREES
>>> � � � MSEC1 MIXING SCHEME WITH 0.019
>>> :ENE �: ********** TOTAL ENERGY IN Ry = � � �-764463.06753755
>>> :DIS �: �CHARGE DISTANCE � � � ( 1.3977454 for atom � 21 spin 2)
>>> �0.6630361
>>> :PLANE: �INTERSTITIAL TOTAL � �108.75537 DISTAN �0.115D+01 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.39365 DISTAN �0.158D+01 %
>>> :DIRM : �MEMORY 8/8 RESCALE �2.793 RED �0.761 PRED �0.410 NEXT �0.520
>>> :DIRP : �|BROYD|= 0.579D+00 |PRATT|= 0.243D+00 ANGLE= � 2.6 DEGREES
>>> :DIRB : �|BROYD|= 0.102D+01 |PRATT|= 0.676D+00 ANGLE= �73.8 DEGREES
>>> � � � MSEC1 MIXING SCHEME WITH 0.025
>>> :ENE �: ********** TOTAL ENERGY IN Ry = � � �-764461.86144927
>>> :DIS �: �CHARGE DISTANCE � � � ( 1.5359856 for atom � 21 spin 2)
>>> �0.6783981
>>> :PLANE: �INTERSTITIAL TOTAL � �103.24631 DISTAN �0.114D+01 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.39129 DISTAN �0.217D+01 %
>>> :DIRM : �MEMORY 8/8 RESCALE �2.901 RED �1.321 PRED �0.520 NEXT �0.404
>>> :DIRP : �|BROYD|= 0.111D+00 |PRATT|= 0.179D+00 ANGLE= � 5.0 DEGREES
>>> :DIRB : �|BROYD|= 0.438D+00 |PRATT|= 0.679D+00 ANGLE= �94.5 DEGREES
>>> � � � MSEC1 MIXING SCHEME WITH 0.019
>>> :ENE �: ********** TOTAL ENERGY IN Ry = � � �-764462.76680261
>>> :DIS �: �CHARGE DISTANCE � � � ( 1.5635417 for atom � 21 spin 2)
>>> �0.6769593
>>> :PLANE: �INTERSTITIAL TOTAL � �102.21850 DISTAN �0.113D+01 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.39069 DISTAN �0.218D+01 %
>>> :DIRM : �MEMORY 8/8 RESCALE �2.856 RED �1.003 PRED �0.404 NEXT �0.393
>>> :DIRP : �|BROYD|= 0.741D-01 |PRATT|= 0.173D+00 ANGLE= �10.2 DEGREES
>>> :DIRB : �|BROYD|= 0.550D+00 |PRATT|= 0.678D+00 ANGLE= �67.7 DEGREES
>>> � � � MSEC1 MIXING SCHEME WITH 0.019
>>> :ENE �: ********** TOTAL ENERGY IN Ry = � � �-764462.80353390
>>> :DIS �: �CHARGE DISTANCE � � � ( 1.3885591 for atom � 21 spin 2)
>>> �0.6168273
>>> :PLANE: �INTERSTITIAL TOTAL � �101.58134 DISTAN �0.114D+01 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.39058 DISTAN �0.127D+01 %
>>> :DIRM : �MEMORY 8/8 RESCALE �2.826 RED �0.617 PRED �0.393 NEXT �0.453
>>> :DIRP : �|BROYD|= 0.333D+01 |PRATT|= 0.278D+00 ANGLE= � 3.0 DEGREES
>>> :DIRB : �|BROYD|= 0.506D+01 |PRATT|= 0.678D+00 ANGLE= �66.0 DEGREES
>>> � � � MSEC1 MIXING SCHEME WITH 0.030
>>> :ENE �: ********** TOTAL ENERGY IN Ry = � � �-764461.99355790
>>> :DIS �: �CHARGE DISTANCE � � � ( 1.1568872 for atom � 14 spin 2)
>>> �0.6685332
>>> :PLANE: �INTERSTITIAL TOTAL � � 73.66428 DISTAN �0.100D+01 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.37899 DISTAN �0.113D+01 %
>>> :DIRM : �MEMORY 8/8 RESCALE �2.827 RED �0.851 PRED �0.453 NEXT �0.536
>>> :DIRP : �|BROYD|= 0.568D-01 |PRATT|= 0.208D+00 ANGLE= � 8.8 DEGREES
>>> :DIRB : �|BROYD|= 0.242D+00 |PRATT|= 0.678D+00 ANGLE= �65.5 DEGREES
>>> � � � MSEC1 MIXING SCHEME WITH 0.036
>>> :ENE �: ********** TOTAL ENERGY IN Ry = � � �-764462.86242784
>>> :DIS �: �CHARGE DISTANCE � � � ( 1.4264538 for atom � 21 spin 2)
>>> �0.4879323
>>> :PLANE: �INTERSTITIAL TOTAL � � 73.25877 DISTAN �0.999D+00 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.37952 DISTAN �0.123D+01 %
>>> :DIRM : �MEMORY 8/8 RESCALE �2.868 RED �1.083 PRED �0.536 NEXT �0.385
>>> :DIRP : �|BROYD|= 0.227D+01 |PRATT|= 0.193D+00 ANGLE= � 5.2 DEGREES
>>> :DIRB : �|BROYD|= 0.315D+01 |PRATT|= 0.679D+00 ANGLE= �69.6 DEGREES
>>> � � � MSEC1 MIXING SCHEME WITH 0.033
>>> :ENE �: ********** TOTAL ENERGY IN Ry = � � �-764461.97659644
>>> :DIS �: �CHARGE DISTANCE � � � ( 1.6982287 for atom � 21 spin 2)
>>> �0.5405554
>>> :PLANE: �INTERSTITIAL TOTAL � � 59.47974 DISTAN �0.742D+00 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.37338 DISTAN �0.204D+01 %
>>> :DIRM : �MEMORY 8/8 RESCALE �2.915 RED �1.595 PRED �0.385 NEXT �0.206
>>> :DIRP : �|BROYD|= 0.140D+01 |PRATT|= 0.743D-01 ANGLE= � 7.8 DEGREES
>>> :DIRB : �|BROYD|= 0.190D+01 |PRATT|= 0.680D+00 ANGLE= �71.7 DEGREES
>>> � � � MSEC1 MIXING SCHEME WITH 0.021
>>> :ENE �: ********** TOTAL ENERGY IN Ry = � � �-764462.61304845
>>> :DIS �: �CHARGE DISTANCE � � � ( 1.4697547 for atom � 21 spin 2)
>>> �0.4979709
>>> :PLANE: �INTERSTITIAL TOTAL � � 53.21152 DISTAN �0.524D+00 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.37088 DISTAN �0.129D+01 %
>>> :DIRM : �MEMORY 8/8 RESCALE �3.211 RED �0.632 PRED �0.206 NEXT �0.429
>>> :DIRP : �|BROYD|= 0.132D+00 |PRATT|= 0.819D-01 ANGLE= 161.5 DEGREES
>>> :DIRB : �|BROYD|= 0.491D+00 |PRATT|= 0.681D+00 ANGLE= �64.0 DEGREES
>>> � � � MSEC1 MIXING SCHEME WITH 0.033
>>> :ENE �: ********** TOTAL ENERGY IN Ry = � � �-764462.19383195
>>> :DIS �: �CHARGE DISTANCE � � � ( 2.2846737 for atom � �2 spin 2)
>>> �0.9802665
>>> :PLANE: �INTERSTITIAL TOTAL � � 53.64758 DISTAN �0.517D+00 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.37173 DISTAN �0.245D+01 %
>>> :DIRM : �MEMORY 8/8 RESCALE �3.366 RED �1.894 PRED �0.429 NEXT �0.216
>>> :DIRP : �|BROYD|= 0.320D-01 |PRATT|= 0.450D-01 ANGLE= 142.6 DEGREES
>>> :DIRB : �|BROYD|= 0.240D+00 |PRATT|= 0.681D+00 ANGLE= �92.6 DEGREES
>>> � � � MSEC1 MIXING SCHEME WITH 0.017
>>> :ENE �: ********** TOTAL ENERGY IN Ry = � � �-764465.78776379
>>> :DIS �: �CHARGE DISTANCE � � � ( 2.0226278 for atom � �2 spin 2)
>>> �0.7593622
>>> :PLANE: �INTERSTITIAL TOTAL � � 53.76097 DISTAN �0.530D+00 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.37277 DISTAN �0.180D+01 %
>>> :DIRM : �MEMORY 8/8 RESCALE �3.627 RED �0.735 PRED �0.216 NEXT �0.318
>>> :DIRP : �|BROYD|= 0.174D+00 |PRATT|= 0.679D-01 ANGLE= �18.9 DEGREES
>>> :DIRB : �|BROYD|= 0.600D+00 |PRATT|= 0.681D+00 ANGLE= �89.4 DEGREES
>>> � � � MSEC1 MIXING SCHEME WITH 0.023
>>> :ENE �: ********** TOTAL ENERGY IN Ry = � � �-764463.66314145
>>> :DIS �: �CHARGE DISTANCE � � � ( 1.7094630 for atom � 21 spin 2)
>>> �0.7114884
>>> :PLANE: �INTERSTITIAL TOTAL � � 53.15388 DISTAN �0.497D+00 %
>>> :CHARG: �CLM CHARGE � TOTAL � � 83.37101 DISTAN �0.220D+01 %
>>> :DIRM : �MEMORY 8/8 RESCALE �3.839 RED �1.225 PRED �0.318 NEXT �0.208
>>> :DIRP : �|BROYD|= 0.111D+01 |PRATT|= 0.544D-01 ANGLE= �19.6 DEGREES
>>> :DIRB : �|BROYD|= 0.140D+01 |PRATT|= 0.682D+00 ANGLE= �72.8 DEGREES
>>> � � � MSEC1 MIXING SCHEME WITH 0.019
>>> :ENE �: ********** TOTAL ENERGY IN Ry = � � �-764464.34795513
>>>
>>
>>
>> --
>> Laurence Marks
>> Department of Materials Science and Engineering
>> MSE Rm 2036 Cook Hall
>> 2220 N Campus Drive
>> Northwestern University
>> Evanston, IL 60208, USA
>> Tel: (847) 491-3996 Fax: (847) 491-7820
>> email: L-marks at northwestern dot edu
>> Web: www.numis.northwestern.edu
>> Chair, Commission on Electron Crystallography of IUCR
>> www.numis.northwestern.edu/
>> Electron crystallography is the branch of science that uses electron
>> scattering and imaging to study the structure of matter.
>>
>
>
>
>--
>Laurence Marks
>Department of Materials Science and Engineering
>MSE Rm 2036 Cook Hall
>2220 N Campus Drive
>Northwestern University
>Evanston, IL 60208, USA
>Tel: (847) 491-3996 Fax: (847) 491-7820
>email: L-marks at northwestern dot edu
>Web: www.numis.northwestern.edu
>Chair, Commission on Electron Crystallography of IUCR
>www.numis.northwestern.edu/
>Electron crystallography is the branch of science that uses electron
>scattering and imaging to study the structure of matter.
>_______________________________________________
>Wien mailing list
>Wien at zeus.theochem.tuwien.ac.at
>http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien