Inspur%20group

1
?????????
????????
Inspur group
2
????????
???? ????
???? NF52201 2146G SAS raid1
???? NF52201 2146G SAS raid1
I/O?? NF52201 2146G SAS raid1
???? NF52202 5300G SAS raid5
???? NX7140N112 64G SSD
??? NF560D22 1146G SAS
?? AS400 81T raid5 (1 ???)
???? H3C?????
???? Qlogic 9120
???? ????
???? RedHat AS 5 update3 (??2.6.18-128)
???/??? Intel C/Fortran ???/ Intel MKL?????
???? Gaussian vasp Wien2k
MPI?? intel mpi 3.1
???? TSJM/PBS
???? ????????2.1
Inspur group
3
???????
??
??
Inspur group
4
????

• ????????
• ?????????
• ??????
• ??????
• ??????
• ?????????
• ?????
• ????????

Inspur group
5
?????????
1. ???????????????????????????????????,???????????
????????????? 2. ??????,?????????????????????????
??????? 3. ????????,?????????????? 4.
???????,???????????,??????????????? 5.
???????????????,??????????/??/??????????????? 6.
????????????????????,???????????,????????????? 7.
?????(?????)???????????????,??????????????(lustre
),???????????????????? 8. ??????????,????????????
?????????,??????????????????? 9.
?????(???)??,??8??????????????
Inspur group
6
??????????
1. ???? SSH ????,?????????????????
??????Putty? 2. ??????? SFTP
????,????FTP?? ??????SecureFX?WinSCP? 3.
?????????? ??mail??,???????????????
?????????? du -kh sort -n ,??????????,???????
Inspur group
7
??????????
4. ??????,?????,???????? 5. ??????????
???????????????,????????????????????????????????
SSH????????exit???????????????
Inspur group
8
??????????

• ????????
• ssh -l (your count) 202.127.207.132
• ???????????
• vi /.bashrc
• source /opt/intel/impi/3.1/bin64/mpivars.sh
• source /opt/intel/cce/10.1.021/bin/iccvars.sh
• source /opt/intel/fce/10.1.021/bin/ifortvars.s
  h
• source /opt/intel/mkl/10.2.2.025/tools/environ
  ment/mklvarsem64t.sh
• ?????
• source /.bashrc
• ???? du -kh sort -n ,??????????

Inspur group
4/10/2018
9
???????
1. ??????????????? /home/lt???gt/ltyouridgt 2
. ???????????????????????????,????????????????????
????,????????????????,???????????????????????? du
-kh sort n???????????????????? 3.
??????????????,??????????,??????,???????????
Inspur group
10
???????
1.????????,?????????????????????????,?????????????
CPU????????,?????????????CPU????I/O????,?????????,
???????????I/O??,????????????? 2.
???????(????????1/4)????????????????? 3.
???????,?????????????,???????????????,??qdel??,
????????????????? 4. ????????????????????????????
?????????????????????????????? 5.
???????(????)?????????,??????(lustre)????????? 6.
??????????????,??????????? vi??????????????????
7. ????????????24GB???????????fuque??
Inspur group
11
???????

• PBS????
• pbs command????????????????
• pbs server ??????????,????/?????????,????????,???
  ?????
• pbs mom???????,?pbs server???????????????????
• scheduler(maui) ????????????

Inspur group
12
???????

• Torque???????
• ??Torque???????
• ????????
• ????????
• PBS??
• qsub ??????
• qstat ??
• qdel ???

Inspur group
13
???????

• PBS????
• ???????
• qsub ??????
• ??????,???????
• ??????
• qstat ??
• ??????
• -q ????????
• -Q???????????
• -an??????????
• -r?????????
• -f jobid?????????
• -Qf queue???????????
• -B??PBS????????

Inspur group
14
???????

• PBS????
• ??????
• qdel ???
• ??????qsub?????????????
• ????
• 1??root????????????????
• 2?????????????????????????,????????????
• 3?root????????
• 4???PBS??????,?????testque?

Inspur group
15
???????

• ???????
• ????
• !/bin/bash
• PBS -d /lustre/ISSP2/dyliu/workdir
• PBS -o /lustre/ISSP2/dyliu/output
• PBS -e /lustre/ISSP2/dyliu/error
• PBS -l nodes2ppn8
• PBS -l walltime2400000
• PBS -l mem4gb
• PBS -q allque

Inspur group
16
???????

• ??MPI??(VASP)
• ulimit -s unlimited
• source /opt/intel/Compiler/11.1/046/bin/intel64/ic
  cvars_intel64.sh
• source /opt/intel/Compiler/11.1/046/bin/intel64/if
  ortvars_intel64.sh
• source /opt/intel/mkl/10.2.2.025/tools/environment
  /mklvarsem64t.sh
• source /opt/intel/impi/3.1/bin64/mpivars.sh
• EXEC/opt/issp2/vasp_4.6.28

Inspur group
17
???????

• ??MPI??(VASP)
• NPcat PBS_NODEFILE wc -l
• NNcat PBS_NODEFILE sort uniq tee
  /tmp/nodes. wc -l
• cat PBS_NODEFILE gt /tmp/nodes.
• sed -i s//-ib8/ /tmp/nodes.
• mpdboot -n NN -f /tmp/nodes. -r ssh
• mpiexec -genv I_MPI_DEVICE rdma -machinefile
  /tmp/nodes. -n NP EXEC
• mpdallexit
• rm -f /tmp/nodes.

Inspur group
18
???????

• ????wien2k
• alias lsi"ls -aslp .in"
• alias lso"ls -aslp .ou"
• alias lsd"ls -aslp .def"
• alias lsc"ls -aslp .cl"
• alias lss"ls -aslp .sc"
• alias lse"ls -aslp .error"
• alias pslapw"ps -ef grep "lapw""
• alias cdw"cd curdir"
• export EDITOR"xterm -e vi"
• export SCRATCHcurdir

Inspur group
19
???????

• ????wien2k
• export WIENROOT/opt/issp2/wien2k
• export W2WEB_CASE_BASEDIRcurdir
• export STRUCTEDIT_PATHWIENROOT/SRC_structeditor
  /bin
• export PDFREADERacroread
• export PATHPATHWIENROOTSTRUCTEDIT_PATH.
• export OCTAVE_EXEC_PATHPATH
• export OCTAVE_PATHSTRUCTEDIT_PATH
• export PATHPATHWIENROOT.
• ulimit -s unlimited
• alias octave"octave -p OCTAVE_PATH"

Inspur group
20
???????

• ????wien2k
• EXEC"/opt/issp2/wien2k/runsp_lapw -ec
  0.00001 -cc 0.00001 -i 400 -p"
• cat PBS_NODEFILE gt nodelist.
• sed -i s//-ib/ nodelist.
• echo "" gt .machines
• echo "granularity1" gtgt .machines
• echo "lapw0"sed -n 1p nodelist. gtgt .machines
• for i in cat nodelist.
• do
• echo "1"i gtgt .machines
• done
• echo "extrafine1" gtgt .machines
• rm -f nodelist.
• EXEC

Inspur group
21
???????

• ????Gaussian
• export GAUSS_EXEDIR/opt/issp2/g03
• export g03root/opt/issp2/
• export PATH/opt/issp2/g03/opt/issp2/g03/linda7.
  2/opteron-linux-I8/binPATH
• export GAUSS_SCRDIR/lustre/ISSP2/dyliu/g03tmp
• export LINDA_PATH/opt/issp2/g03/linda7.2/opteron
  -linux-I8
• source /opt/issp2/g03/bsd/g03.profile
• /opt/issp2/g03 lt FILENAME

Inspur group
22
???????

• ????????
• ???????,??????autofs,20?????,??????,??,????,???
  ????,??????????
• ??????
• VASP
• Wien2k
• g03
• castep
• dmol3
• espresso

Inspur group
23
???????
????

• ????

• ????(1)

Inspur group
24
???????
????

• ????(2)

• ????(3)

Inspur group
25
???????
????

• ????

Inspur group
26
???????
1. ????lustre????????I/O??,??????,?????????,??????
??,??,??????????????,????????????????? 2.
???????????????,???????????????,?????,????????,???
???????? 3. ???????????,??????(??????????),?????
????? 4. ????????????????????????????????????????
?????????????????? 5. ????(lustre)????????,?????,
????????????????,???????????,??????????? 6.
??????????????,?????,??????????????
Inspur group
27
???????
1. ???? /lustre/lt???gt/yourid (???9.6TB
,????????,??????????,?????????,30??????????) 2.
???? /home/lt???gt/yourid (??????????50GB,???????
?,????,????????)
Inspur group
28
??????????
1. ?????????????,??? /opt ?,???Intel
????MPI????? 2. ??????????????? /opt/lt???gt ???
3. ???????????,????????????,?????????????,???????
????,??????????,????????????? 4.
???,??????????,????????.bashrc??,???????????? 5.
?????,???????????????????? 6. ???????????????
Inspur group
29
??????????
?????????? vi /.bashrc g03
export GAUSS_EXEDIR/opt/issp2/g03 export
g03root/opt/issp2 export PATH/opt/issp2/g03//o
pt/issp2/g03/linda7.2/opteron-linux-I8/binPATH e
xport GAUSS_SCRDIR/lustre/ISSP2/ltyouridgt export
LINDA_PATH/opt/issp2/g03/linda7.2/opteron-linux-I
8 source /opt/issp2/g03/bsd/g03.profile
intel source /opt/intel/impi/3.1/bin64/mp
ivars.sh source /opt/intel/cce/10.1.021/bin/iccvar
s.sh source /opt/intel/fce/10.1.021/bin/ifortvars.
sh source /opt/intel/mkl/10.2.2.025/tools/environm
ent/mklvarsem64t.sh
Inspur group
30
??????????
?? ?? ????
Intel C/C Compiler (32bit/64bit) 10.1.021 /opt/intel/cc/10.1.021 /opt/intel/cce/10.1.021
Intel C/C Compiler 11.1.046 /opt/intel/Compiler/11.1/046/
Intel Fortran Compiler (32bit/64bit) 10.1.021 /opt/intel/fc/10.1.021 /opt/intel/fce/10.1.021
Intel Fortran Compiler 11.1.046 /opt/intel/Compiler/11.1/046/
Intel MKL 9.1.018 /opt/intel/mkl/9.1.018
Intel MKL 10.1.2.024 /opt/intel/mkl/10.1.2.024
Intel MKL 10.2.2.025 /opt/intel/mkl/10.2.2.025
Intel MPI 3.1 /opt/intel/impi/3.1
Perl 5.8.8 /usr/bin
Python 2.4.3 /usr/bin
Inspur group
31
??????????
?????????????/opt/lt???gt???,?issp2
?? ?? ????
Gaussian E01 /opt/issp2/g03
VASP 4.6.26 /opt/issp2/vasp
Material Studio 4.4 /opt/issp2/Accelrys/MaterialsStudio44
wien2k /opt/issp2/wien2k
Inspur group
32
??????
1. ???????????????,?????,?????????,???????????????
????????? 2. ???????,???????????????????????????
????,???????????????????,??????????????,????????(?
?????????)????????????
Inspur group
33
?????????
1. ?? 13739223032 2. ??
dyliu_at_theory.issp.ac.cn gywu_at_theory.issp.ac
.cn
Inspur group
34
A
Inspur group
35
????!
Inspur group
4/10/2018
Inspur group