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I setup a samba server (Version 3.6.9-167.el6_5). One of the sub folder contains more than one thousand, if I delete this folder then I can connect to the server, otherwise I am getting a timeout error (NT_STATUS_IO_TIMEOUT). How can I prevent this error? Is it scanning the whole file system during connection?

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Someone reporting the same problem as yourself in this thread titled: Samba NT_STATUS_IO_TIMEOUT [solved] reported the following fixed their issue:

/etc/smb.conf

[global]
    workgroup = METRAN
    encrypt passwords = yes
    wins support = yes
    log level = 1 
    max log size = 1000
    read only = no
[homes] 
    browsable = no
    map archive = yes
[printers] 
    path = /var/tmp
    printable = yes
    min print space = 2000
[test]
    browsable = yes
    read only = yes
    path = /usr/local/samba/tmp
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    Which part of that file fixed the problem. – buhtz Jan 8 '18 at 14:48
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I was getting NT_STATUS_IO_TIMEOUT transferring large files with a slow windows-2000 samba share over a slow network connection.

The error would not occur after reducing the buffer size, for example to 8192: An example from the command line:

smbclient //192.168.0.2/spool -b 8192 -c "put bigfile.pdf"
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What filesystem do you have here ? Could you try mounting filesystem as read only

Try changing

\HKLM\SYSTEM\CurrentControlSet\Services\LanmanWorkstation\Parameters\

to higher value (for timeouts)

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