Hi All,
I tried to build a Linux node myself, but I encountered problems.
My environment:
Phoenix client:
Operating system: Windows10
Phoenix version: Phoenix 8.1
Linux server:
Operating system: CentOS Linux 7
IP: 192.168.31.130
Installed software: epel-release, gcc, R, ksh, libxml2-devel, nfs-utils, rpcbind, torque-4.2.9.tar.gz, openssl-devel, boost-devel, libtool-y
R version: 3.5.2
The following R packages are installed: batchtools, XML, reshape, Certara.NLME8
Mounted shared directory: mount -t nfs 192.168.31.130: /var/tmp/nlme /mnt
The TORQUE job control software is installed.
[root@master /]# qnodes
cn1
state = free
np = 2
ntype = cluster
status = rectime=1560150776,varattr=,jobs=,state=free,netload=491676,gres=,loadave=0.00,ncpus=2,physmem=3865308kb,availmem=5562644kb,totmem=5962456kb,idletime=655,nusers=2,nsessions=4,sessions=1543 1555 1605 1677,uname=Linux cn1 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64,opsys=linux
mom_service_port = 15002
mom_manager_port = 15003
master
state = free
np = 2
ntype = cluster
status = rectime=1560150774,varattr=,jobs=,state=free,netload=284510000,gres=,loadave=0.00,ncpus=2,physmem=3865308kb,availmem=4256656kb,totmem=5962456kb,idletime=74353,nusers=3,nsessions=3,sessions=1654 1498 29642,uname=Linux master 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64,opsys=linux
mom_service_port = 15002
mom_manager_port = 15003
scene 1:
Configuration: 192.168.31.130|Linux|MultiCore|test3||/mnt|/bin/R|2|
1.1 In the "simple" and "Predictive" Run mode, I can submit the NLME task to Linux. Linux can complete the task calculation, and the result can be returned to Phoenix from Linux.
1.2 In the "Bootstrap" Run mode, I can submit the NLME task to Linux. Linux can complete the task calculation, but the Phoenix client confirms that it is running, and the result is not returned to Phoenix.
You can see all the results of the calculation in the Linux directory.
But the Phoenix client always shows "Running NLME on system"
View the file "DME_BO~1.619-496/NlmeRemote.LOG" in the Linux shared directory to get the following information:
nohup: 忽略输入
/usr/bin/R
Rscript /mnt/InstallDirNLME/bootstrap.r MultiCore /mnt /mnt/DME_BO~1.619-496 3 1000 2 2 test.mdl cols1.txt data1.txt 9316 nlmeargs.txt nlmeargs.txt test.mdl nlmeargs.txt cols1.txt data1.txt test.mdl 2 95
WORKING_DIR=/mnt/NLME173ac7f6fe137/NLME173ac12b7b585,MPIFLAG=MPINO, LOCAL_HOST=NO,NUM_NODES=1,SHARED_DRIVE=
model=test.mdl, nlmeDir=/mnt/InstallDirNLME
Deleting files
-------------------------------------------------------------
-------------------- Translating --------------------------
/mnt/InstallDirNLME/TDL4 /hash 1408304074 /L ./test.mdl ./Work
Done
-------------------------------------------------------------
------------------- Compliling *.c -------------------------
-------------------------------------------------------------
----------------------- Linking -----------------------------
-------------------------------------------------------------
ln: 无法创建符号链接"/mnt/NLME173ac7f6fe137/NLME173ac12b7b585/NLME7.exe": 文件已存在
NULL
Warning messages:
1: In stuff[row] <- currentList : 被替换的项目不是替换值长度的倍数
2: In stuff[row] <- currentList : 被替换的项目不是替换值长度的倍数
1.3 In the "Cov.Srch.Stepwise" Run mode, I can submit the NLME task to Linux. Linux can complete the task calculation, but the Phoenix client confirms that it is running, and the result is not returned to Phoenix.
You can see all the results of the calculation in the Linux directory.
But the Phoenix client always shows "Running NLME on system"
View the file "DME_SI~1.512-480/NlmeRemote.LOG" in the Linux shared directory to get the following information:
nohup: 忽略输入
/usr/bin/R
Rscript /mnt/InstallDirNLME/stepwise_covarsrch.r MultiCore /mnt/InstallDirNLME /mnt /mnt/DME_SI~1.512-480 test.mdl nlmeargs.txt test.mdl cols1.txt data1.txt nlmeargs.txt 3 V-wt V-apgr Ke-wt -2LL:1,1,1 0.01 0.001 2 Pheno Model
WORKING_DIR=/mnt/NLME16aa821e9ed02/NLME16aa87e37534d,MPIFLAG=MPINO, LOCAL_HOST=NO,NUM_NODES=1,SHARED_DRIVE=
model=test.mdl, nlmeDir=/mnt/InstallDirNLME
Deleting files
-------------------------------------------------------------
-------------------- Translating --------------------------
/mnt/InstallDirNLME/TDL4 /hash 1408304609 /L ./test.mdl ./Work
Done
-------------------------------------------------------------
------------------- Compliling *.c -------------------------
-------------------------------------------------------------
----------------------- Linking -----------------------------
-------------------------------------------------------------
unix2dos: converting file /mnt/NLME16aa821e9ed02/NLME16aa87e37534d/jobs/01/1//out000.txt to DOS format ...
unix2dos: converting file /mnt/NLME16aa821e9ed02/NLME16aa87e37534d/jobs/02/2//out100.txt to DOS format ...
unix2dos: converting file /mnt/NLME16aa821e9ed02/NLME16aa87e37534d/jobs/03/3//out010.txt to DOS format ...
unix2dos: converting file /mnt/NLME16aa821e9ed02/NLME16aa87e37534d/jobs/04/4//out001.txt to DOS format ...
WORKING_DIR=/mnt/NLME16aa8771a8725/NLME16aa83f361009,MPIFLAG=MPINO, LOCAL_HOST=NO,NUM_NODES=1,SHARED_DRIVE=
model=test.mdl, nlmeDir=/mnt/InstallDirNLME
Deleting files
-------------------------------------------------------------
-------------------- Translating --------------------------
/mnt/InstallDirNLME/TDL4 /hash 1408304609 /L ./test.mdl ./Work
Done
-------------------------------------------------------------
------------------- Compliling *.c -------------------------
-------------------------------------------------------------
----------------------- Linking -----------------------------
-------------------------------------------------------------
unix2dos: converting file /mnt/NLME16aa8771a8725/NLME16aa83f361009/jobs/01/1//out110.txt to DOS format ...
unix2dos: converting file /mnt/NLME16aa8771a8725/NLME16aa83f361009/jobs/02/2//out101.txt to DOS format ...
[1] "/mnt/NLME16aa821e9ed02" "/mnt/NLME16aa8771a8725"
Scene 2:
Configuration: 192.168.31.130|Linux|TORQUE|test4||/mnt|/bin/R|2|
In this scenario, any "run mode" cannot be completed.
In the "simple" and "Predictive" modes, I can submit the NLME task to Linux. Linux can complete the task calculation, but the Phoenix client confirms that it is running and the result is not returned to Phoenix..
2.1 In the simple and Predictive mode, I can submit the NLME task to Linux. Linux can complete the task calculation, but the calculation result cannot return to Phoenix from Linux.
You can see all the results of the calculation in the Linux directory.
But the Phoenix client always shows "Running NLME on system"
DME_SI~1.113-909/NlmeRemote.LOG:
/usr/bin/R
Rscript /mnt/InstallDirNLME/generic_run.r COVAR_SEARCH TORQUE /mnt/InstallDirNLME /mnt /mnt/DME_SI~1.113-909 nlmeControlFile.txt 2 SingleNlme
载入需要的程辑包:data.table
No readable configuration file found
Created registry in '/mnt/NLME157711491531c/NLME15771147abe8c/registry' using cluster functions 'Interactive'
WORKING_DIR=/mnt/NLME157711491531c/NLME15771147abe8c,MPIFLAG=MPINO, LOCAL_HOST=NO,NUM_NODES=1,SHARED_DRIVE=
model=test.mdl, nlmeDir=/mnt/InstallDirNLME
Deleting files
-------------------------------------------------------------
-------------------- Translating --------------------------
/mnt/InstallDirNLME/TDL4 /hash 1408305253 /L ./test.mdl ./Work
Done
-------------------------------------------------------------
------------------- Compliling *.c -------------------------
-------------------------------------------------------------
----------------------- Linking -----------------------------
-------------------------------------------------------------
Adding 1 jobs ...
Submitting 1 jobs in 1 chunks using cluster functions 'TORQUE' ...
unix2dos: converting file /mnt/NLME157711491531c/NLME15771147abe8c/../out000001.txt to DOS format ...
unix2dos: converting file /mnt/NLME157711491531c/NLME15771147abe8c/../nlme7engine.log to DOS format ...
[1] "removeRegistry() AGAIN"
[1] "/mnt/NLME157711491531c"