SGE faild提交作业，属性不是内存值

Question

我未能提交具有mem属性的作业。由于我是新手，谷歌两天后，我在这里寻求帮助。任何建议将不胜感激！

以下是我所做的：

\ 1。提交我的稿子：

qsub -S /bin/bash -A assembly -pe threads 16 -l mem=2GB -cwd -N "pBcR_correct_asm" -j y -o /dev/null runCorrection.sh 

Unable to run job: unknown resource "mem". 
Exiting. 

\ 2。考虑到我已经将“h”替换为“主机”，根据SGE unknown resource "nodes"解决了我的问题，我将“m”替换为“mem”，并且它不起作用。

\ 3.在google之后，我知道“h” 为在 “/选择/ gridengine/util的/资源/森特里/ 主机名” 中定义的快捷方式，并且可以与 “的qconf -sc” 予以确认：

qconf -sc 

#name    shortcut type  relop requestable consumable default urgency 
#---------------------------------------------------------------------------------------- 
arch    a   RESTRING == YES   NO   NONE  0 
calendar   c   RESTRING == YES   NO   NONE  0 
cpu     cpu  DOUBLE  >= YES   NO   0  0 
display_win_gui  dwg  BOOL  == YES   NO   0  0 
h_core    h_core  MEMORY  <= YES   NO   0  0 
h_cpu    h_cpu  TIME  <= YES   NO   0:0:0 0 
h_data    h_data  MEMORY  <= YES   NO   0  0 
h_fsize    h_fsize MEMORY  <= YES   NO   0  0 
h_rss    h_rss  MEMORY  <= YES   NO   0  0 
h_rt    h_rt  TIME  <= YES   NO   0:0:0 0 
h_stack    h_stack MEMORY  <= YES   NO   0  0 
h_vmem    h_vmem  MEMORY  <= YES   NO   0  0 
hostname   h   HOST  == YES   NO   NONE  0 
load_avg   la   DOUBLE  >= NO   NO   0  0 
load_long   ll   DOUBLE  >= NO   NO   0  0 
load_medium   lm   DOUBLE  >= NO   NO   0  0 
load_short   ls   DOUBLE  >= NO   NO   0  0 
m_core    core  INT   <= YES   NO   0  0 
m_socket   socket  INT   <= YES   NO   0  0 
m_topology   topo  RESTRING == YES   NO   NONE  0 
m_topology_inuse utopo  RESTRING == YES   NO   NONE  0 
mem_free   mf   MEMORY  <= YES   NO   0  0 
mem_total   mt   MEMORY  <= YES   NO   0  0 
mem_used   mu   MEMORY  >= YES   NO   0  0 

\ 4因此我代替。 “mt”改为“mem”，但是它抱怨属性问题，根据上面的输出，似乎mem_total与之前的“hostname”几乎相同，那么我认为jsv在通过SGE指南后可能会出现问题，但我找不到任何脚本包含“无法运行作业：属性......” ，其中“/ opt/gridengine/util/resources/jsv”的负责人。我想我必须配置一些文件，但是这些文件是什么，我该怎么办？

qsub -S /bin/bash -A assembly -pe threads 16 -l mt=2GB -cwd -N "pBcR_correct_asm" -j y -o test.out runCorrection.sh 

Unable to run job: attribute "mem_total" is not a memory value. 
Exiting. 

Answer 1

你可能想要的是h_vmem。至少这是我总是用来指​​定我想要的工作请求的内存的属性。

参见：

http://gridscheduler.sourceforge.net/htmlman/htmlman5/queue_conf.html?pathrev=V62u5_TAG

具体来说，

 The resource limit parameters s_vmem and h_vmem are imple- 
    mented by Sun Grid Engine as a job limit. They impose a 
    limit on the amount of combined virtual memory consumed by 
    all the processes in the job. If h_vmem is exceeded by a job 
    running in the queue, it is aborted via a SIGKILL signal 
    (see kill(1)). If s_vmem is exceeded, the job is sent a 
    SIGXCPU signal which can be caught by the job. If you wish 
    to allow a job to be "warned" so it can exit gracefully 
    before it is killed then you should set the s_vmem limit to 
    a lower value than h_vmem. For parallel processes, the 
    limit is applied per slot which means that the limit is mul- 
    tiplied by the number of slots being used by the job before 
    being applied. 

此外，您可能需要设置为消耗使用qconf。

Answer 2

@Vince！

非常感谢您的回复。

最后我解决了我的问题，通过使用“h_vmem = 2g”（“2GB”会给出错误），但我不知道在哪里可以找到如何设计复杂值（MEMORY）的值。

以下信息现在是不必要的。

我已经读过你给的网站，并将h_vmem和s_vmeme的属性复杂地配置为“可使用”，但它不起作用。我想我必须配置当前“无”队列的“complex_value”。但是，我无法打开可能会告诉我如何配置的网络http://gridscheduler.sourceforge.net/htmlman/htmlman5/sge_types.html?pathrev=V62u5_TAG。我有权配置队列吗？我是否也必须配置主机？

任何建议将不胜感激！

Fowllowing是我做过的：

\ 1。将h_vmem和s_vmem的消耗品属性更改为“YES”：

qconf -sc 

#name    shortcut type  relop requestable consumable default urgency 
#---------------------------------------------------------------------------------------- 
arch    a   RESTRING == YES   NO   NONE  0 
calendar   c   RESTRING == YES   NO   NONE  0 
cpu     cpu  DOUBLE  >= YES   NO   0  0 
display_win_gui  dwg  BOOL  == YES   NO   0  0 
h_core    h_core  MEMORY  <= YES   NO   0  0 
h_cpu    h_cpu  TIME  <= YES   NO   0:0:0 0 
h_data    h_data  MEMORY  <= YES   NO   0  0 
h_fsize    h_fsize MEMORY  <= YES   NO   0  0 
h_rss    h_rss  MEMORY  <= YES   NO   0  0 
h_rt    h_rt  TIME  <= YES   NO   0:0:0 0 
h_stack    h_stack MEMORY  <= YES   NO   0  0 
h_vmem    h_vmem  MEMORY  <= YES   YES  0  0 
hostname   h   HOST  == YES   NO   NONE  0 
load_avg   la   DOUBLE  >= NO   NO   0  0 
load_long   ll   DOUBLE  >= NO   NO   0  0 
load_medium   lm   DOUBLE  >= NO   NO   0  0 
load_short   ls   DOUBLE  >= NO   NO   0  0 
m_core    core  INT   <= YES   NO   0  0 
m_socket   socket  INT   <= YES   NO   0  0 
m_topology   topo  RESTRING == YES   NO   NONE  0 
m_topology_inuse utopo  RESTRING == YES   NO   NONE  0 
mem_free   mf   MEMORY  <= YES   NO   0  0 
mem_total   mt   MEMORY  <= YES   NO   0  0 
mem_used   mu   MEMORY  >= YES   NO   0  0 
min_cpu_interval mci  TIME  <= NO   NO   0:0:0 0 
np_load_avg   nla  DOUBLE  >= NO   NO   0  0 
np_load_long  nll  DOUBLE  >= NO   NO   0  0 
np_load_medium  nlm  DOUBLE  >= NO   NO   0  0 
np_load_short  nls  DOUBLE  >= NO   NO   0  0 
num_proc   p   INT   == YES   NO   0  0 
qname    q   RESTRING == YES   NO   NONE  0 
rerun    re   BOOL  == NO   NO   0  0 
s_core    s_core  MEMORY  <= YES   NO   0  0 
s_cpu    s_cpu  TIME  <= YES   NO   0:0:0 0 
s_data    s_data  MEMORY  <= YES   NO   0  0 
s_fsize    s_fsize MEMORY  <= YES   NO   0  0 
s_rss    s_rss  MEMORY  <= YES   NO   0  0 
s_rt    s_rt  TIME  <= YES   NO   0:0:0 0 
s_stack    s_stack MEMORY  <= YES   NO   0  0 
s_vmem    s_vmem  MEMORY  <= YES   YES  0  0 
seq_no    seq  INT   == NO   NO   0  0 
slots    s   INT   <= YES   YES  1  1000 
swap_free   sf   MEMORY  <= YES   NO   0  0 
swap_rate   sr   MEMORY  >= YES   NO   0  0 
swap_rsvd   srsv  MEMORY  >= YES   NO   0  0 
swap_total   st   MEMORY  <= YES   NO   0  0 
swap_used   su   MEMORY  >= YES   NO   0  0 
tmpdir    tmp  RESTRING == NO   NO   NONE  0 
virtual_free  vf   MEMORY  <= YES   NO   0  0 
virtual_total  vt   MEMORY  <= YES   NO   0  0 
virtual_used  vu   MEMORY  >= YES   NO   0  0 
# >#< starts a comment but comments are not saved across edits -------- 

\ 2。将我的作业提交到smp队列。q，它抱怨同样的问题：

qsub -S /bin/bash -A assembly -q smp.q -pe newPe 16 -l h_vmem=2GB -cwd -N "pBcR_correct_asm" -j y -o runCorrection.sh 

Unable to run job: attribute "h_vmem" is not a memory value. 
Exiting. 

\ 3。 smp.q.的信息我认为“complex_values”应该改变，“h_vmem”可以保持不变：

qconf -sq smp.q 

qname     smp.q 
hostlist    @smp.q 
seq_no    0 
load_thresholds  np_load_avg=1.75 
suspend_thresholds NONE 
nsuspend    1 
suspend_interval  00:05:00 
priority    0 
min_cpu_interval  00:05:00 
processors   UNDEFINED 
qtype     BATCH INTERACTIVE 
ckpt_list    NONE 
pe_list    make newPe 
rerun     FALSE 
slots     160 
tmpdir    /tmp 
shell     /bin/csh 
prolog    NONE 
epilog    NONE 
shell_start_mode  posix_compliant 
starter_method  NONE 
suspend_method  NONE 
resume_method   NONE 
terminate_method  NONE 
notify    00:00:60 
owner_list   NONE 
user_lists   NONE 
xuser_lists   NONE 
subordinate_list  NONE 
complex_values  NONE 
projects    NONE 
xprojects    NONE 
calendar    NONE 
initial_state   default 
s_rt     INFINITY 
h_rt     INFINITY 
s_cpu     INFINITY 
h_cpu     INFINITY 
s_fsize    INFINITY 
h_fsize    INFINITY 
s_data    INFINITY 
h_data    INFINITY 
s_stack    INFINITY 
h_stack    INFINITY 
s_core    INFINITY 
h_core    INFINITY 
s_rss     INFINITY 
h_rss     INFINITY 
s_vmem    INFINITY 
h_vmem    INFINITY 

\ 4。 @ smp.q中的主机信息：

qconf -sconf smp03.local 

#smp03.local: 
mailer      /bin/mail 
xterm      /usr/bin/X11/xterm 
execd_spool_dir    /opt/gridengine/default/spool 

\ 5。全球信息。我在这里添加h_vmem和s_vmem吗？

qconf -sconf 

#global: 
execd_spool_dir    /opt/gridengine/default/spool 
mailer      /bin/mail 
xterm      /usr/bin/X11/xterm 
load_sensor     none 
prolog      none 
epilog      none 
shell_start_mode    posix_compliant 
login_shells     sh,ksh,csh,tcsh 
min_uid      0 
min_gid      0 
user_lists     none 
xuser_lists     none 
projects      none 
xprojects     none 
enforce_project    false 
enforce_user     auto 
load_report_time    00:00:40 
max_unheard     00:05:00 
reschedule_unknown   00:00:00 
loglevel      log_warning 
administrator_mail   none 
set_token_cmd    none 
pag_cmd      none 
token_extend_time   none 
shepherd_cmd     none 
qmaster_params    none 
execd_params     ENABLE_ADDGRP_KILL=TRUE H_MEMORYLOCKED=infinity 
reporting_params    accounting=true reporting=true \ 
          flush_time=00:00:15 joblog=true sharelog=00:00:00 
finished_jobs    100 
gid_range     20000-20100 
qlogin_command    builtin 
qlogin_daemon    builtin 
rlogin_command    builtin 
rlogin_daemon    builtin 
rsh_command     builtin 
rsh_daemon     builtin 
max_aj_instances    2000 
max_aj_tasks     75000 
max_u_jobs     0 
max_jobs      0 
max_advance_reservations  0 
auto_user_oticket   0 
auto_user_fshare    0 
auto_user_default_project none 
auto_user_delete_time  86400 
delegated_file_staging  false 
reprioritize     0 
jsv_url      none 
jsv_allowed_mod    ac,h,i,e,o,j,M,N,p,w