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Connection to qiita.ucsd.edu timed out. #130

Open kattweigh2 opened 6 months ago

kattweigh2 commented 6 months ago

Hi there,

I installed redbiom using conda: conda install -c conda-forge redbiom To trial, I ran the example command: redbiom search metadata beer | head

But received the error attached. It appears it's timing out trying to connect to qiita.ucsd.edu Apologies if this is a user/firewall issue but if you could give any suggestion of the cause of the issue that would be great!

Thanks :)

stderr.txt

wasade commented 6 months ago

Thanks, could you try the command again? We have occasional timeouts which we haven't traced fully, and the command is working on my end

kattweigh2 commented 6 months ago

Thanks for your quick response! Just tried again and received the same error. I've tried it multiple times over the past week and have tried on two different HPCs with the same error message every time :/

wasade commented 6 months ago

That's odd, I wonder if the systems are blocking outbound on the port used. Can you send the output from traceroute qiita.ucsd.edu?

kattweigh2 commented 6 months ago

traceroute to qiita.ucsd.edu (169.228.46.28), 30 hops max, 60 byte packets 1 _gateway (10.199.147.21) 1.115 ms 2 10.199.144.22 (10.199.144.22) 0.096 ms 0.096 ms 0.085 ms 3 ip-10-215-162-193.ap-southeast-2.compute.internal (10.215.162.193) 48.534 ms 48.529 ms 48.523 ms 4 ip-10-215-168-105.ap-southeast-2.compute.internal (10.215.168.105) 4.217 ms 4.215 ms 4.204 ms 5 ip-10-215-168-106.ap-southeast-2.compute.internal (10.215.168.106) 3.359 ms 3.337 ms 3.339 ms 6 ip-10-215-173-126.ap-southeast-2.compute.internal (10.215.173.126) 4.256 ms 4.219 ms 4.261 ms 7 10.0.32.5 (10.0.32.5) 10.155 ms 5.781 ms 7.891 ms 8 192.168.67.113 (192.168.67.113) 3.797 ms 3.801 ms 3.783 ms 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30

wasade commented 6 months ago

Thanks. It looks like your connections bounce around a lot on internal networks. Are you able to, from that host, connect to Qiita?

wasade commented 6 months ago

Can you ping google?

kattweigh2 commented 5 months ago

Hopefully I've done this correctly...

From the command: ping qiita.ucsd.edu I received: PING qiita.ucsd.edu (169.228.46.28) 56(84) bytes of data. 64 bytes from qiita.ucsd.edu (169.228.46.28): icmp_seq=1 ttl=41 time=151 ms 64 bytes from qiita.ucsd.edu (169.228.46.28): icmp_seq=2 ttl=41 time=148 ms 64 bytes from qiita.ucsd.edu (169.228.46.28): icmp_seq=3 ttl=41 time=149 ms 64 bytes from qiita.ucsd.edu (169.228.46.28): icmp_seq=4 ttl=41 time=148 ms 64 bytes from qiita.ucsd.edu (169.228.46.28): icmp_seq=5 ttl=41 time=148 ms 64 bytes from qiita.ucsd.edu (169.228.46.28): icmp_seq=6 ttl=41 time=149 ms 64 bytes from qiita.ucsd.edu (169.228.46.28): icmp_seq=7 ttl=41 time=150 ms 64 bytes from qiita.ucsd.edu (169.228.46.28): icmp_seq=8 ttl=41 time=148 ms 64 bytes from qiita.ucsd.edu (169.228.46.28): icmp_seq=9 ttl=41 time=148 ms 64 bytes from qiita.ucsd.edu (169.228.46.28): icmp_seq=10 ttl=41 time=149 ms 64 bytes from qiita.ucsd.edu (169.228.46.28): icmp_seq=11 ttl=41 time=148 ms 64 bytes from qiita.ucsd.edu (169.228.46.28): icmp_seq=12 ttl=41 time=148 ms 64 bytes from qiita.ucsd.edu (169.228.46.28): icmp_seq=13 ttl=41 time=149 ms etc....

From ping google.com: PING google.com (142.250.66.206) 56(84) bytes of data. 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=1 ttl=112 tim e=6.88 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=2 ttl=112 tim e=5.26 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=3 ttl=112 tim e=6.93 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=4 ttl=112 tim e=5.73 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=5 ttl=112 tim e=5.35 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=6 ttl=112 tim e=5.29 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=7 ttl=112 tim e=5.28 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=8 ttl=112 tim e=5.51 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=9 ttl=112 tim e=5.31 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=10 ttl=112 ti me=5.28 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=11 ttl=112 ti me=5.40 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=12 ttl=112 ti me=5.57 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=13 ttl=112 ti me=5.64 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=14 ttl=112 ti me=5.35 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=15 ttl=112 time=5.51 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=16 ttl=112 time=5.34 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=17 ttl=112 time=5.44 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=18 ttl=112 time=5.50 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=19 ttl=112 time=5.50 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=20 ttl=112 time=5.39 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=21 ttl=112 time=5.36 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=22 ttl=112 time=5.88 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=23 ttl=112 time=5.57 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=24 ttl=112 time=5.61 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=25 ttl=112 time=6.75 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=26 ttl=112 time=7.58 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=27 ttl=112 time=5.40 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=28 ttl=112 time=5.24 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=29 ttl=112 time=6.05 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=30 ttl=112 time=5.70 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=31 ttl=112 time=6.67 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=32 ttl=112 time=6.23 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=33 ttl=112 time=5.40 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=34 ttl=112 time=5.51 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=35 ttl=112 time=5.82 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=36 ttl=112 time=5.35 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=37 ttl=112 time=5.34 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=38 ttl=112 time=5.23 ms 64 bytes from syd09s23-in-f14.1e100.net (142.250.66.206): icmp_seq=39 ttl=112 time=5.95 ms etc...

kattweigh2 commented 5 months ago

Extra info...

I then got these stats:

--- qiita.ucsd.edu ping statistics --- 258 packets transmitted, 258 received, 0% packet loss, time 257309ms rtt min/avg/max/mdev = 147.635/148.431/154.227/0.846 ms

--- google.com ping statistics --- 713 packets transmitted, 712 received, 0.140252% packet loss, time 713133ms rtt min/avg/max/mdev = 5.200/5.820/26.180/1.603 ms

And this from curl rather than ping: Command: curl -I qiita.ucsd.edu HTTP/1.1 301 Moved Permanently Server: nginx/1.24.0 Date: Sun, 10 Mar 2024 22:20:42 GMT Content-Type: text/html Content-Length: 169 Connection: keep-alive Location: https://qiita.ucsd.edu/

Command: curl -I https://qiita.ucsd.edu/ HTTP/1.1 200 OK Server: nginx/1.24.0 Date: Sun, 10 Mar 2024 22:21:02 GMT Content-Type: text/html; charset=UTF-8 Content-Length: 0 Connection: keep-alive Etag: "da39a3ee5e6b4b0d3255bfef95601890afd80709"

wasade commented 5 months ago

Thanks! Does redbiom work from a system that is not part of the HPC environment? It is possible the system administrators are blocking outbound traffic on port 7329.

Could you send the output of curl -v http://qiita.ucsd.edu:7329/get/foo please?

kattweigh2 commented 5 months ago

curl -v http://qiita.ucsd.edu:7329/get/foo

wasade commented 5 months ago

Could you contact the system administrator and inquire about this? You can cc me too if helpful @.)On Mar 10, 2024, at 17:31, kattweigh2 @.> wrote: curl -v http://qiita.ucsd.edu:7329/get/foo

Trying 169.228.46.28:7329... connect to 169.228.46.28 port 7329 failed: Connection timed out Failed to connect to qiita.ucsd.edu port 7329 after 130926 ms: Connection timed out Closing connection 0 curl: (28) Failed to connect to qiita.ucsd.edu port 7329 after 130926 ms: Connection timed out

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kattweigh2 commented 5 months ago

Thanks very much for your help! Have just sent an email with you CC'd. Cheers :)

Bas-Voermans commented 3 months ago

I'm inquiring about this issue because i am running into the exact same thing. Was there a solution found?

wasade commented 3 months ago

Hi @Bas-Voermans, in this case, outbound traffic on port 7329 was being blocked by @kattweigh2's network administrators. It is also possible a timeout could just occur by chance. Can you try running redbiom summarize contexts to see if it triggers a timeout? If it does timeout, then could you email me at "damcdonald AT ucsd.edu"?