Salmon 1.1.0 auto update check stalled

[cihanerkut]

salmon command gives as expected:

salmon v1.1.0

Usage:  salmon -h|--help or
        salmon -v|--version or
        salmon -c|--cite or
        salmon [--no-version-check] <COMMAND> [-h | options]

Commands:
     index Create a salmon index
     quant Quantify a sample
     alevin single cell analysis
     swim  Perform super-secret operation
     quantmerge Merge multiple quantifications into a single file

However, salmon index --help freezes without any CPU usage. strace shows it's trying to connect to an IP address, which belongs to GitHub but out of commission right now.

socket(AF_INET, SOCK_STREAM, IPPROTO_TCP) = 6
epoll_ctl(4, EPOLL_CTL_ADD, 6, {EPOLLIN|EPOLLPRI|EPOLLERR|EPOLLHUP|EPOLLET, {u32=509961152, u64=140196832437184}}) = 0
ioctl(6, FIONBIO, [1])                  = 0
connect(6, {sa_family=AF_INET, sin_port=htons(80), sin_addr=inet_addr("185.199.108.153")}, 16) = -1 EINPROGRESS (Operation now in progress)
epoll_ctl(4, EPOLL_CTL_MOD, 6, {EPOLLIN|EPOLLPRI|EPOLLOUT|EPOLLERR|EPOLLHUP|EPOLLET, {u32=509961152, u64=140196832437184}}) = 0
epoll_wait(4, ^Cstrace: Process 4488 detached

Waiting long enough, it tries another IP address, which is also broken.

My Salmon is compiled with GCC 8.2.0 / gompi2019a toolset using EasyBuild. It runs on Centos 7.

Passing --no-version-check solves the problem but this option isn't displayed on main help screen, I found it somewhere in the source.

[cihanerkut]

The same with version 1.2.0.

Is there a way to disable version check by default, completely? I install Salmon as a module and I wouldn't let it update itself automatically, anyway.

[rob-p]

Hi @cihanerkut,

First, thanks for reporting this, and going through the trouble to give the strace information. Second, salmon won't auto-update anyway. That would be quite slick, but there's not a good and reliable way to do that with natively-compiled programs that I know of.

However, the most surprising thing is that you are finding the call to the version check ip to be hanging for any significant amount of time. The timeout should be pretty quick. How long does it hang when you do salmon index --help? I'll look into it on our end as well.

[cihanerkut]

Hi @rob-p,

The first attempt timed out in 2 min 7 sec.

22:06:42 socket(AF_INET, SOCK_STREAM, IPPROTO_TCP) = 6
22:06:42 epoll_ctl(4, EPOLL_CTL_ADD, 6, {EPOLLIN|EPOLLPRI|EPOLLERR|EPOLLHUP|EPOLLET, {u32=497378240, u64=139780208026560}}) = 0
22:06:42 ioctl(6, FIONBIO, [1])         = 0
22:06:42 connect(6, {sa_family=AF_INET, sin_port=htons(80), sin_addr=inet_addr("185.199.109.153")}, 16) = -1 EINPROGRESS (Operation now in progress)
22:06:42 epoll_ctl(4, EPOLL_CTL_MOD, 6, {EPOLLIN|EPOLLPRI|EPOLLOUT|EPOLLERR|EPOLLHUP|EPOLLET, {u32=497378240, u64=139780208026560}}) = 0
22:06:42 epoll_wait(4, [{EPOLLIN|EPOLLOUT|EPOLLERR|EPOLLHUP, {u32=497378240, u64=139780208026560}}], 128, -1) = 1
22:08:49 poll([{fd=6, events=POLLOUT}], 1, 0) = 1 ([{fd=6, revents=POLLOUT|POLLERR|POLLHUP}])
22:08:49 getsockopt(6, SOL_SOCKET, SO_ERROR, [110], [4]) = 0
22:08:49 close(6)                       = 0

[EricDeveaud]

The same with version 1.2.0.

Is there a way to disable version check by default, completely? I install Salmon as a module and I wouldn't let it update itself automatically, anyway.

--- Salmon.cpp.ori  2020-04-21 15:12:29.916219870 +0000
+++ Salmon.cpp  2020-04-21 15:16:48.488926415 +0000
@@ -53,7 +53,7 @@
       "Usage:  salmon -h|--help or \n"
       "        salmon -v|--version or \n"
       "        salmon -c|--cite or \n"
-      "        salmon [--no-version-check] <COMMAND> [-h | options]\n\n");
+      "        salmon <COMMAND> [-h | options]\n\n");
   helpMsg.write("Commands:\n");
   helpMsg.write("     index Create a salmon index\n");
   helpMsg.write("     quant Quantify a sample\n");
@@ -171,8 +171,6 @@
     // https://gist.github.com/randomphrase/10801888
     po::options_description sfopts("Allowed Options");
     sfopts.add_options()("version,v", "print version string")(
-        "no-version-check",
-        "don't check with the server to see if this is the latest version")(
         "cite,c", "show citation information")(
         "help,h", "produce help message")("command", po::value<string>(),
                                           "command to run {index, quant, sf}")(
@@ -209,11 +207,6 @@
       std::exit(0);
     }

-    if (!vm.count("no-version-check")) {
-      std::string versionMessage = getVersionMessage();
-      std::cerr << versionMessage;
-    }
-
     // po::notify(vm);

     std::string cmd = vm["command"].as<std::string>();

[EricDeveaud]

I would have prefered an option to check if a new version is available instead of having a software that systematicly phone home

it will be problematic on our cluster as compute nodes does not have network acces to internet.
did not checked yet how this case in handled by salmon

regards

Eric

[rob-p]

@EricDeveaud,

Does passing --no-version-check resolve the issue? This flag goes before any other command and disables this behavior. For example:

salmon --no-version-check index -t <gentrome.fa> -d decoys.txt -i index

or

salmon --no-version-check quant -i index -la -1 reads_1.fq.gz -2 reads_2.fq.gz -o quant_dir

There should be no network access when using this flag.

[EricDeveaud]

yes --no-version-check does the trick, but among all the users of the cluster I'm pretty sure some of them will forgot ;-)

on our local installation I disabled the getVersionMessage even if salmon handle the no network cleanly. (I tested using unshare -n salmon whatever you want)
NB debian maintainer also disabled the phone home call in their packages

sorry if it it may sound harsh

[cihanerkut]

Just an idea. Would it be possible to assign an environment variable, such as SALMON_NO_VERSION_CHECK, whose existence overrides version checking? This wouldn't break compatibility with older scripts because they wouldn't have the variable in the first place. In non-networked nodes, an admin can simply set this variable and users will run salmon as usual.

[rob-p]

@cihanerkut,

Yes; this is a nice solution and I think it wouldn't be too hard!

[rob-p]

@cihanerkut and @EricDeveaud,

We just released 1.2.1, which is on the release page, and dockerhub, and should propagate to bioconda soon. It adds support for the SALMON_NO_VERSION_CHECK environment variable. If you set SALMON_NO_VERSION_CHECK to either 1 or TRUE in the environment where salmon is running, it will skip the version check. I hope this helps!

--Rob

[EricDeveaud]

thanks

[cihanerkut]

Thank you very much!