VENUS/NWCHEM7 installation

[HS]

Hello, 

I am new to install VENUS/NWCHEM7. I installed NWCHEM7 with the install script that I have attached. After that, at the stage to install VENUS, I have got the following error: 

..../nwchem7/src/tools/install/lib/libarmci.a(comex.o): undefined reference to symbol 'shm_unlink@@GLIBC_2.2.5'

//lib/x86_64-linux-gnu/librt.so.1: error adding symbols: DSO missing from command line

collect2: error: ld returned 1 exit status

Makefile:49: recipe for target 'ven_nw.e' failed

make: *** [ven_nw.e] Error 1

May I get some help to fix the problem? Any help would be greatly appreciated. 

Thank you very much. 

Best regards, 

HS

[Edoardo Aprà]

Could you try to execute the attached link-nwchem7.sh script?

This script will execute just the link step with slightly modified options.

Please post the complete output of the script if linking is still failing

[HS]

I tried to execute the attached link-nwchem7.sh script as you suggested. I got an error when I used sh to execute the script with the following error:

install.sh: 20: export: -lrt: bad variable name

So, I used bash to execute the script. And I got the error message. Please find the file attached. 

Thank you. 

Best regards, 

HS

2021년 2월 5일 금요일 오후 1시 16분 9초 UTC-6에 Edoardo Aprà님이 작성:

[Edoardo Aprà]

I can't tell what is going on with your latest problem.

Please use the attached modified version of your original script. It is a bash script.

This script will remove the old compilation files and re-compile from scratch

Please post the full log file.

[HS]

I used the modified script and am posting the full log file. Please find attached. Thank you. 

Best regards, 

HS

2021년 2월 5일 금요일 오후 3시 5분 15초 UTC-6에 Edoardo Aprà님이 작성:

[Edoardo Aprà]

I don't see any problem in the log file, do you?

[HS]

No, I don't see any problem here. My main goal is to install venus/nwchem. So, after that, I tried to install the venus part from the result. 

And I got the error message as same as I posted firstly. 

/usr/bin/ld: /home/hs/nwchem7/src/tools/install/lib/libarmci.a(comex.o): undefined reference to symbol 'shm_unlink@@GLIBC_2.2.5'

//lib/x86_64-linux-gnu/librt.so.1: error adding symbols: DSO missing from command line

collect2: error: ld returned 1 exit status

Makefile:49: recipe for target 'ven_nw.e' failed

make: *** [ven_nw.e] Error 1

Thank you. 

Best regards, 

Hyunsik Kim

2021년 2월 5일 금요일 오후 5시 29분 33초 UTC-6에 Edoardo Aprà님이 작성:

[Edoardo Aprà]

You might want to contact the Venus developers for this problem.

The installation script you posted seemed to be using just the NWChem source code.

[HS]

Yes, I am attaching the installation script for the nwchem installation and the gentinterface set up as well. 

For the venus installation, I have used the following:

gfortran -m64 -ffast-math  -Warray-bounds -fdefault-integer-8 -fno-tree-dominator-opts  -finline-functions -L/home/hs/opt/openmpi/lib  -O2 -g -fno-aggressive-loop-optimizations -fno-tree-dominator-opts  -g -O  ADAMSM.o ANGVEL.o AXT.o BAREXC.o CENMAS.o CUBEND.o DANGLE.o DMBE.o DVDQ.o EBOND.o EIGN.o EIGOUT.o ENERGY.o ENMODE.o vFDATE.o FGMTRX.o FINAL.o FINLNJ.o FMTRX.o GAMA.o GFINAL.o MPATHO.o GHOST.o GINROT.o GLPAR.o GPATH.o GRCONV.o GWRITE.o HALPHA.o HBEND.o HEXP.o HFD.o HNONB.o HOMOQP.o HTAU.o INITEBK.o INITQP.o LENJ.o LEPS1.o LEPS2.o LMEXCT.o LMODE.o MORSE.o MPATH.o NMODE.o ORTHAN.o PARSN2.o PARTI.o POTEN.o RAND0.o RAND1.o RANDST.o READPT.o RELAX.o ROTATE.o ROTEN.o ROTN.o RUNGEK.o RYDBG.o SELECT.o STRET.o SURF.o SYBMOL.o TEST.o TETRA.o THRMAN.o VENUS.o VRR.o VRT.o VSN2.o VTT.o WEBOND.o WENMOD.o WLBOND.o STATPT.o HEIGHT.o CPUSEC.o RADAU.o SYMPLE.o lnb.o thermo.o thermbath.o gasdev.o CRCO6.o POTENZ.o hessint.o verlet.o JMAXCALC.o PROBJ.o DENQ.o QMMICRO.o MICROCI.o VOLPSCONE.o QMCALC.o NWCHEM_LINK.o -L/home/hs/nwchem7/lib/LINUX64 -L/home/hs/nwchem7/src/tools/install/lib  -o ven_nw.e /home/hs/nwchem7/src/stubs.o -lgeninterface -lnwcutil -lnwctask -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lddscf -lguess -lhessian -lvib -lnwcutil -lproperty -lnwints -lbq -lcons -lperfm -lnwcutil -lga -lpeigs -lperfm -lcons -lbq -lnwcutil  -llapack -lblas -larmci -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lopenblas -lopenblas -lpthread

/usr/bin/ld: /home/nammika/nwchem7/src/tools/install/lib/libarmci.a(comex.o): undefined reference to symbol 'shm_unlink@@GLIBC_2.2.5'

//lib/x86_64-linux-gnu/librt.so.1: error adding symbols: DSO missing from command line

collect2: error: ld returned 1 exit status

Makefile:49: recipe for target 'ven_nw.e' failed

make: *** [ven_nw.e] Error 1

Thank you. 

Best regards, 

HS

2021년 2월 5일 금요일 오후 5시 40분 54초 UTC-6에 Edoardo Aprà님이 작성:

[Edoardo Aprà]

Replace

-lopenblas

with

-lopenblas -lrt

[HS]

Thank you for the instruction. I have tried as suggested with the option "-lopenblas -lrt". But it still has the same problem. 

Best regards, 

HS

2021년 2월 5일 금요일 오후 5시 58분 41초 UTC-6에 Edoardo Aprà님이 작성:

[Edoardo Aprà]

There is something really odd in your linking sequence.

You have installed NWChem under /home/hs/nwchem7/src/, therefore libarmci.a  should be found in /home/hs/nwchem7/src/tools/install/lib/libarmci.a. Instead, the link is using libarmci.a uses /home/nammika/nwchem7/src/tools/install/lib/libarmci.a .

Do you have a symbolic link between /home/nammika/ and /home/hs/ or are they separate directories?

[Hyunsik Kim]

It was a typo. All the work was done in the same directory, /home/hs/. 

Thank you. 

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