年假结束，第一件事情就是之前的metemap已经下载好了，三个安装包（需要提前注册时间长，才能下载到这三个安装包）

image.png
跟着教程进行安装时，https://metamap.nlm.nih.gov/MetaMapLite.shtml
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最后一句怎么都不成功

14:53:09 jiarongf@172.16.10.223:/data1/jiarongf/Knowledge_Graph/metamap/metamap_bag/bag/public_mm_lite
$
./metamaplite.sh --indexdir=data/ivf/2020AA/Base file
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...
Exception in thread "main" java.io.FileNotFoundException: file (No such file or directory)
        at java.io.FileInputStream.open0(Native Method)
        at java.io.FileInputStream.open(FileInputStream.java:195)
        at java.io.FileInputStream.<init>(FileInputStream.java:138)
        at gov.nih.nlm.nls.metamap.document.FreeText.loadFile(FreeText.java:73)
        at gov.nih.nlm.nls.metamap.document.FreeText.loadFreeTextFile(FreeText.java:137)
        at gov.nih.nlm.nls.metamap.document.FreeText.loadFileAsBioCDocumentList(FreeText.java:157)
        at gov.nih.nlm.nls.ner.MetaMapLite.main(MetaMapLite.java:1536)

一直报错，看到前面的官网说需要jdk1.8：To run MetaMapLite, you will need the Java Runtime Environment (JRE). We have tested MetaMapLite with JRE 1.8. The JRE is available from: http://www.java.com，所以我把java版本降到8，还是不行，依旧报错，
这是因为有文件找不到，于是打开metamaplite.sh一个一个的找，发现其中的dir数据集的目录是AA的data/ivf/2020AA/USAbase，直接换掉data/ivf/2020AA/Base file，也不知道行不行，
安装完man在运行这个./metamaplite.sh --indexdir=data/ivf/2020AA/Base file，还是报错

15:26:38 jiarongf@172.16.10.223:/data1/jiarongf/Knowledge_Graph/metamap/metamap_bag/bag/public_mm_lite
$
./metamaplite.sh --indexdir=data/ivf/2020AA/Base file
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...
Exception in thread "main" java.io.FileNotFoundException: file (No such file or directory)
        at java.io.FileInputStream.open0(Native Method)
        at java.io.FileInputStream.open(FileInputStream.java:195)
        at java.io.FileInputStream.<init>(FileInputStream.java:138)
        at gov.nih.nlm.nls.metamap.document.FreeText.loadFile(FreeText.java:73)
        at gov.nih.nlm.nls.metamap.document.FreeText.loadFreeTextFile(FreeText.java:137)
        at gov.nih.nlm.nls.metamap.document.FreeText.loadFileAsBioCDocumentList(FreeText.java:157)
        at gov.nih.nlm.nls.ner.MetaMapLite.main(MetaMapLite.java:1536)
15:26:52 jiarongf@172.16.10.223:/data1/jiarongf/Knowledge_Graph/metamap/metamap_bag/bag/public_mm_lite

step2.

安装main的时候，

Public MetaMap basedir: /data1/jiarongf/Knowledge_Graph/metamap/metamap_bag/bag/public_mm
Public MetaMap Program Dir: /data1/jiarongf/Knowledge_Graph/metamap/metamap_bag/bag/public_mm/bin
Java Home dir: /data1/jiarongf/software/jdl/jdk1.8.0_281

https://metamap.nlm.nih.gov/Installation.shtml
运行的时候有一个报错

15:49:32 jiarongf@172.16.10.223:/data1/jiarongf/Knowledge_Graph/metamap/metamap_bag/bag/public_mm
$
./bin/metamap
/data1/jiarongf/Knowledge_Graph/metamap/metamap_bag/bag/public_mm/bin/SKRrun.20 /data1/jiarongf/Knowledge_Graph/metamap/metamap_bag/bag/public_mm/bin/metamap20.BINARY.Linux --lexicon db -Z 2020AA
Berkeley DB databases (USAbase 2020AA strict model) are open.
Static variants will come from table varsan in /data1/jiarongf/Knowledge_Graph/metamap/metamap_bag/bag/public_mm/DB/DB.USAbase.2020AA.strict.
Derivational Variants: Adj/noun ONLY.
Variant generation mode: static.

### MetaMap ERROR: Calling socket_client_open for TAGGER Server on host localhost and port 1795:
error(system_error,system_error(SPIO_E_NET_CONNREFUSED))

解决方法

15:49:39 jiarongf@172.16.10.223:/data1/jiarongf/Knowledge_Graph/metamap/metamap_bag/bag/public_mm
$
./bin/skrmedpostctl start
$Starting skrmedpostctl:
started.
15:52:36 jiarongf@172.16.10.223:/data1/jiarongf/Knowledge_Graph/metamap/metamap_bag/bag/public_mm
$
./bin/metamap
/data1/jiarongf/Knowledge_Graph/metamap/metamap_bag/bag/public_mm/bin/SKRrun.20 /data1/jiarongf/Knowledge_Graph/metamap/metamap_bag/bag/public_mm/bin/metamap20.BINARY.Linux --lexicon db -Z 2020AA
Berkeley DB databases (USAbase 2020AA strict model) are open.
Static variants will come from table varsan in /data1/jiarongf/Knowledge_Graph/metamap/metamap_bag/bag/public_mm/DB/DB.USAbase.2020AA.strict.
Derivational Variants: Adj/noun ONLY.
Variant generation mode: static.
Established connection $stream(139631136340016) to TAGGER Server on localhost.

metamap (2020)

Control options:
  composite_phrases=4
  lexicon=db
  mm_data_year=2020AA
|:

简单来说运行一共三步，首先进入/data1/jiarongf/Knowledge_Graph/metamap/metamap_bag/bag/public_mm目录，
接着运行./bin/skrmedpostctl start
./bin/metamap
./bin/wsdserverctl stop就可以了

!!!!另外如果main什么都不输出的话，重新运行一下上面的那三步就可以了