# PBM-agent on docker running into "storage is not initialized" **URL:** \ **Category:** Percona Backup for MongoDB\ **Tags:** percona, mongodb\ **Created:** [April 8, 2025, 1:02pm UTC](https://forums.percona.com/t/pbm-agent-on-docker-running-into-storage-is-not-initialized/37534 "2025-04-08T13:02:01Z")\ **Posts on this page:** 14\ **Page:** 1
**Author:** ![miwalk](https://avatars.discourse-cdn.com/v4/letter/m/9de053/32.png) [@miwalk](https://forums.percona.com/u/miwalk)\ **Post date:** [April 8, 2025, 1:02pm UTC](https://forums.percona.com/t/pbm-agent-on-docker-running-into-storage-is-not-initialized/37534/1 "2025-04-08T13:02:01Z")
Hi, I’ve tried to go trough docs, but didn’t find correct information. I’ve selected to build a image on which I will be able to run PBM backups. 1. Guide in [Run in Docker - Percona Backup for MongoDB](https://docs.percona.com/percona-backup-mongodb/install/docker.html#prerequisites), contains wrong information about the images & packages. The “example” doesn’t contain required packages: pbm: /lib64/libc.so.6: version `GLIBC_2.32' not found (required by pbm) pbm: /lib64/libc.so.6: version `GLIBC\_2.34’ not found (required by pbm) So I decided to build image using following docker file ```auto FROM percona/percona-server-mongodb:latest AS mdb FROM percona/percona-backup-mongodb:latest AS pbm FROM debian:bookworm-slim RUN apt-get update && \ apt-get install -y --no-install-recommends \ libgssapi-krb5-2 \ libkrb5-3 \ libcurl4 \ ca-certificates \ libldap-common \ ldap-utils \ && rm -rf /var/lib/apt/lists/* RUN mkdir -p /data/db /data/configdb COPY --from=mdb /usr/bin/mongod /usr/bin/ COPY --from=pbm /usr/bin/pbm* /usr/bin/ CMD ["tail", "-f", "/dev/null"] ``` 1. Container with the image deployed, PBM started using pbm config --file /etc/percona-backup/pbm\_config.yaml` This is the what file contains: storage: type: filesystem filesystem: path: /backups I see that PBM started OK, but now I need to perform backup. Started 3 processes for all MongoDB nodes on the same docker image using: 'pbm-agent --mongodb-uri “mongodb://XXX:XXX@mongodb-0.mongodb:27017/?authSource=admin&replicaSet=rs0” Unfortunately, pbm-agent returns: 2025-04-08T12:30:53Z W [rs0/mongodb-0.mongodb:27017] [agentCheckup] storage is not initialized pbm-agent doesn’t offer --config flag, are you able to explain why I am getting " storage is not initialized"? ---
**Author:** ![radoslaw.szulgo](https://sea1.discourse-cdn.com/flex019/user_avatar/forums.percona.com/radoslaw.szulgo/32/17315_2.png) [@radoslaw.szulgo](https://forums.percona.com/u/radoslaw.szulgo)\ **Post date:** [April 8, 2025, 1:04pm UTC](https://forums.percona.com/t/pbm-agent-on-docker-running-into-storage-is-not-initialized/37534/2 "2025-04-08T13:04:40Z")
Are you sure you have started you MongoDB nodes in the ReplicaSet topology? ---
**Author:** ![miwalk](https://avatars.discourse-cdn.com/v4/letter/m/9de053/32.png) [@miwalk](https://forums.percona.com/u/miwalk)\ **Post date:** [April 8, 2025, 1:06pm UTC](https://forums.percona.com/t/pbm-agent-on-docker-running-into-storage-is-not-initialized/37534/3 "2025-04-08T13:06:50Z")
Yes, MongoDB server works in ReplicaSet. ---
**Author:** ![Ivan\_Groenewold](https://sea1.discourse-cdn.com/flex019/user_avatar/forums.percona.com/ivan_groenewold/32/6299_2.png) [@Ivan\_Groenewold](https://forums.percona.com/u/Ivan_Groenewold)\ **Post date:** [April 8, 2025, 1:57pm UTC](https://forums.percona.com/t/pbm-agent-on-docker-running-into-storage-is-not-initialized/37534/4 "2025-04-08T13:57:57Z")
Hi, the Example docker image uses `oraclelinux:8` image which includes the dependencies so it does not contain wrong information. In your case you have configured a slim image which comes with minimum packages so it is expected you are missing some dependencies. Now related to your error, PBM requires a shared storage (all nodes need to see the same volume or bucket) please check the steps to [add a remote storage](https://docs.percona.com/percona-backup-mongodb/install/backup-storage.html#procedure) for more details. ---
**Author:** ![Vadim\_Yalovets](https://sea1.discourse-cdn.com/flex019/user_avatar/forums.percona.com/vadim_yalovets/32/43_2.png) [@Vadim\_Yalovets](https://forums.percona.com/u/Vadim_Yalovets)\ **Post date:** [April 8, 2025, 2:12pm UTC](https://forums.percona.com/t/pbm-agent-on-docker-running-into-storage-is-not-initialized/37534/5 "2025-04-08T14:12:01Z")
> [@miwalk](#): > > ```auto > FROM percona/percona-server-mongodb:latest AS mdb > FROM percona/percona-backup-mongodb:latest AS pbm > > FROM debian:bookworm-slim > > ``` Percona images are based on redhat/ubi9-minimal. Could you replace debian image by oraclelinux:9 ? ![Screenshot 2025-04-08 at 16.59.21](https://us1.discourse-cdn.com/flex019/uploads/percona1/original/3X/1/b/1b81c89ce9a08c49084e108f6bc02457a006f68b.png) ---
**Author:** ![miwalk](https://avatars.discourse-cdn.com/v4/letter/m/9de053/32.png) [@miwalk](https://forums.percona.com/u/miwalk)\ **Post date:** [April 9, 2025, 1:23pm UTC](https://forums.percona.com/t/pbm-agent-on-docker-running-into-storage-is-not-initialized/37534/6 "2025-04-09T13:23:12Z")
My MakeFile: ```auto FROM percona/percona-server-mongodb:latest AS mdb FROM percona/percona-backup-mongodb:latest AS pbm FROM oraclelinux:9 RUN mkdir -p /data/db /data/configdb COPY --from=mdb /usr/bin/mongod /usr/bin/ COPY --from=pbm /usr/bin/pbm* /usr/bin/ CMD ["tail", "-f", "/dev/null"] ``` My pbm\_config.yaml → ```auto storage: type: filesystem filesystem: path: /backups ``` Note: /backups is a directory, mounted as PV → ~10Gi pbm status command result: ```auto [root@percona-backup-mongodb-6c47d4555c-bh2gn /]# pbm status Cluster: ======== rs0: - mongodb-0.mongodb.svc.cluster.local.:27017 [P]: pbm-agent [v2.9.1] OK - mongodb-1.mongodb.svc.cluster.local.:27017 [S]: pbm-agent [v2.9.1] OK - mongodb-2.mongodb.svc.cluster.local.:27017 [S]: pbm-agent [v2.9.1] OK PITR incremental backup: ======================== Status [OFF] Currently running: ================== (none) Backups: ======== FS /backups Snapshots: 2025-04-09T06:13:41Z 0.00B [ERROR: Backup stuck at `starting` stage, last beat ts: 1744179222] [2025-04-09T06:13:42Z] ``` pbm config: ```auto [root@percona-backup-mongodb-6c47d4555c-bh2gn /]# pbm config storage: type: filesystem filesystem: path: /backups pitr: enabled: false compression: s2 backup: oplogSpanMin: 0 compression: s2 restore: {} ``` pbm-agent logs from the backup attempt: ```auto 2025-04-09T13:22:00.000+0000 I got command backup [name: 2025-04-09T13:21:59Z, compression: s2 (level: default)] , opid: 67f674775adaf96af16f5d86 Wed, Apr 9 2025 3:22:00 pm2025-04-09T13:22:00.000+0000 I got epoch {1744179172 5} Wed, Apr 9 2025 3:22:00 pm2025-04-09T13:22:00.000+0000 E [backup/2025-04-09T13:21:59Z] node check: full physical backup works since Percona Server for MongoDB 4.2.15, 4.4.6 Wed, Apr 9 2025 3:22:00 pm2025-04-09T13:22:00.000+0000 I [backup/2025-04-09T13:21:59Z] node is not suitable for backup Wed, Apr 9 2025 3:22:00 pm2025-04-09T13:22:00.000+0000 D [backup/2025-04-09T13:21:59Z] init backup meta Wed, Apr 9 2025 3:22:00 pm2025-04-09T13:22:00.000+0000 D [backup/2025-04-09T13:21:59Z] nomination list for rs0: [] Wed, Apr 9 2025 3:22:00 pm2025-04-09T13:22:00.000+0000 I got command backup [name: 2025-04-09T13:21:59Z, compression: s2 (level: default)] , opid: 67f674775adaf96af16f5d86 Wed, Apr 9 2025 3:22:00 pm2025-04-09T13:22:00.000+0000 I got command backup [name: 2025-04-09T13:21:59Z, compression: s2 (level: default)] , opid: 67f674775adaf96af16f5d86 Wed, Apr 9 2025 3:22:00 pm2025-04-09T13:22:00.000+0000 I got epoch {1744179172 5} Wed, Apr 9 2025 3:22:00 pm2025-04-09T13:22:00.000+0000 I got epoch {1744179172 5} Wed, Apr 9 2025 3:22:00 pm2025-04-09T13:22:00.000+0000 E [backup/2025-04-09T13:21:59Z] node check: full physical backup works since Percona Server for MongoDB 4.2.15, 4.4.6 Wed, Apr 9 2025 3:22:00 pm2025-04-09T13:22:00.000+0000 E [backup/2025-04-09T13:21:59Z] node check: full physical backup works since Percona Server for MongoDB 4.2.15, 4.4.6 Wed, Apr 9 2025 3:22:09 pm2025-04-09T13:22:09.000+0000 W [agentCheckup] storage is not initialized Wed, Apr 9 2025 3:22:14 pm2025-04-09T13:22:14.000+0000 W [agentCheckup] storage is not initialized Wed, Apr 9 2025 3:22:14 pm2025-04-09T13:22:14.000+0000 W [agentCheckup] storage is not initialized Wed, Apr 9 2025 3:22:15 pm2025-04-09T13:22:15.000+0000 D [backup/2025-04-09T13:21:59Z] nomination timeout Wed, Apr 9 2025 3:22:15 pm2025-04-09T13:22:15.000+0000 D [backup/2025-04-09T13:21:59Z] skip after nomination, probably started by another node Wed, Apr 9 2025 3:22:29 pm2025-04-09T13:22:29.000+0000 W [agentCheckup] storage is not initialized Wed, Apr 9 2025 3:22:29 pm2025-04-09T13:22:29.000+0000 W [agentCheckup] storage is not initialized ``` Note: MongoDB runs in replicaSet, version of Mongodb: v7.0.5 ---
**Author:** ![miwalk](https://avatars.discourse-cdn.com/v4/letter/m/9de053/32.png) [@miwalk](https://forums.percona.com/u/miwalk)\ **Post date:** [April 9, 2025, 1:28pm UTC](https://forums.percona.com/t/pbm-agent-on-docker-running-into-storage-is-not-initialized/37534/7 "2025-04-09T13:28:05Z")
It looks for me that pbm-agent either lacks `pbm-agent --config` (same as pbm) or lacks access to the storage. But I think you could introduce` pbm-agent config` to check what storage agent has configured. Or it’s some different issue (my configuration problem) which is causing this? ---
**Author:** ![miwalk](https://avatars.discourse-cdn.com/v4/letter/m/9de053/32.png) [@miwalk](https://forums.percona.com/u/miwalk)\ **Post date:** [April 9, 2025, 1:42pm UTC](https://forums.percona.com/t/pbm-agent-on-docker-running-into-storage-is-not-initialized/37534/8 "2025-04-09T13:42:00Z")
I’ve solved problem with storage. There must be a delay between setting pbm config file and starting pbm-agents. Here is a script snip: ```auto echo "Setting up storage" pbm config --file /etc/percona-backup/pbm_config.yaml echo "Waiting 30 seconds before starting pbm-agents..." sleep 30 echo "Setting up pbm-agent 1" ``` Thanks to that, there is no longer an error about storage. But, I’m unable to perform backup: ```auto 2025-04-09T13:36:41.000+0000 I got command backup [name: 2025-04-09T13:36:41Z, compression: s2 (level: default)] , opid: 67f677e9d56c927f4c86be26 Wed, Apr 9 2025 3:36:41 pm2025-04-09T13:36:41.000+0000 I got command backup [name: 2025-04-09T13:36:41Z, compression: s2 (level: default)] , opid: 67f677e9d56c927f4c86be26 Wed, Apr 9 2025 3:36:41 pm2025-04-09T13:36:41.000+0000 I got epoch {1744205727 3} 2025-04-09T13:36:41.177142031Z 2025-04-09T13:36:41.000+0000 I got epoch {1744205727 3} Wed, Apr 9 2025 3:36:41 pm2025-04-09T13:36:41.000+0000 E [backup/2025-04-09T13:36:41Z] node check: full physical backup works since Percona Server for MongoDB 4.2.15, 4.4.6 Wed, Apr 9 2025 3:36:41 pm2025-04-09T13:36:41.000+0000 E [backup/2025-04-09T13:36:41Z] node check: full physical backup works since Percona Server for MongoDB 4.2.15, 4.4.6 Wed, Apr 9 2025 3:36:41 pm2025-04-09T13:36:41.000+0000 I [backup/2025-04-09T13:36:41Z] node is not suitable for backup Wed, Apr 9 2025 3:36:41 pm2025-04-09T13:36:41.000+0000 D [backup/2025-04-09T13:36:41Z] init backup meta Wed, Apr 9 2025 3:36:41 pm2025-04-09T13:36:41.000+0000 D [backup/2025-04-09T13:36:41Z] nomination list for rs0: [] Wed, Apr 9 2025 3:36:42 pm2025-04-09T13:36:42.000+0000 I got command backup [name: 2025-04-09T13:36:41Z, compression: s2 (level: default)] , opid: 67f677e9d56c927f4c86be26 Wed, Apr 9 2025 3:36:42 pm2025-04-09T13:36:42.000+0000 I got epoch {1744205727 3} Wed, Apr 9 2025 3:36:42 pm2025-04-09T13:36:42.000+0000 E [backup/2025-04-09T13:36:41Z] node check: full physical backup works since Percona Server for MongoDB 4.2.15, 4.4.6 Wed, Apr 9 2025 3:36:56 pm2025-04-09T13:36:56.000+0000 D [backup/2025-04-09T13:36:41Z] nomination timeout Wed, Apr 9 2025 3:36:56 pm2025-04-09T13:36:56.000+0000 D [backup/2025-04-09T13:36:41Z] skip after nomination, probably started by another node ``` Does it mean that I’ve to setup Percona Server on cluster, click in the Percona Server UI to perform backup with specific I don’t know pod/container/server agent and then I should be able to perform backups? ---
**Author:** ![miwalk](https://avatars.discourse-cdn.com/v4/letter/m/9de053/32.png) [@miwalk](https://forums.percona.com/u/miwalk)\ **Post date:** [April 9, 2025, 1:46pm UTC](https://forums.percona.com/t/pbm-agent-on-docker-running-into-storage-is-not-initialized/37534/9 "2025-04-09T13:46:21Z")
And - I’ve solved final problem. So, in my setup `pbm backup --type=logical` works. But for` pbm backup --type=physical` → I’m getting `error Wed, Apr 9 2025 3:36:42 pm2025-04-09T13:36:42.000+0000 E [backup/2025-04-09T13:36:41Z] node check: full physical backup works since Percona Server for MongoDB 4.2.15, 4.4.6` Which tells me that I need Percona Server to perform physical backup. I think it’s missing in your docs. ---
**Author:** ![radoslaw.szulgo](https://sea1.discourse-cdn.com/flex019/user_avatar/forums.percona.com/radoslaw.szulgo/32/17315_2.png) [@radoslaw.szulgo](https://forums.percona.com/u/radoslaw.szulgo)\ **Post date:** [April 9, 2025, 2:11pm UTC](https://forums.percona.com/t/pbm-agent-on-docker-running-into-storage-is-not-initialized/37534/10 "2025-04-09T14:11:10Z")
> [@miwalk](#): > > node check: full physical backup works since Percona Server for MongoDB 4.2.15, 4.4.6 Seems PBM cannot retrieve the version from MongoDB. Most likely gets empty string and interprets as the old version. Can you check with mongosh: ```auto db.runCommand( { buildInfo: 1 } ) ``` ---
**Author:** ![miwalk](https://avatars.discourse-cdn.com/v4/letter/m/9de053/32.png) [@miwalk](https://forums.percona.com/u/miwalk)\ **Post date:** [April 18, 2025, 10:12am UTC](https://forums.percona.com/t/pbm-agent-on-docker-running-into-storage-is-not-initialized/37534/11 "2025-04-18T10:12:10Z")
> [@radoslaw.szulgo](#): > > ```auto > db.runCommand( > { > buildInfo: 1 > } > ) > > ``` Nothing special in return, but still - logical backup works, while physical doesn’t. ```auto { version: '7.0.8', gitVersion: 'c5d33e55ba38d98e2f48765ec4e55338d67a4a64', modules: [], allocator: 'tcmalloc', javascriptEngine: 'mozjs', sysInfo: 'deprecated', versionArray: [7, 0, 8, 0], openssl: { running: 'OpenSSL 3.0.11 19 Sep 2023', compiled: 'OpenSSL 3.0.9 30 May 2023' }, buildEnvironment: { distmod: 'debian12', distarch: 'x86_64', cc: '/opt/mongodbtoolchain/v4/bin/gcc: gcc (GCC) 11.3.0', ccflags: '-Werror -include mongo/platform/basic.h -ffp-contract=off -fasynchronous-unwind-tables -g2 -Wall -Wsign-compare -Wno-unknown-pragmas -Winvalid-pch -gdwarf-5 -fno-omit-frame-pointer -fno-strict-aliasing -O2 -march=sandybridge -mtune=generic -mprefer-vector-width=128 -Wno-unused-local-typedefs -Wno-unused-function -Wno-deprecated-declarations -Wno-unused-const-variable -Wno-unused-but-set-variable -Wno-missing-braces -fstack-protector-strong -gdwarf64 -Wa,--nocompress-debug-sections -fno-builtin-memcmp -Wimplicit-fallthrough=5', cxx: '/opt/mongodbtoolchain/v4/bin/g++: g++ (GCC) 11.3.0', cxxflags: '-Woverloaded-virtual -Wpessimizing-move -Wno-maybe-uninitialized -fsized-deallocation -Wno-deprecated -std=c++20', linkflags: '-Wl,--fatal-warnings -B/opt/mongodbtoolchain/v4/bin -gdwarf-5 -pthread -Wl,-z,now -fuse-ld=lld -fstack-protector-strong -gdwarf64 -Wl,--build-id -Wl,--hash-style=gnu -Wl,-z,noexecstack -Wl,--warn-execstack -Wl,-z,relro -Wl,--compress-debug-sections=none -Wl,-z,origin -Wl,--enable-new-dtags', target_arch: 'x86_64', target_os: 'linux', cppdefines: 'SAFEINT_USE_INTRINSICS 0 PCRE2_STATIC NDEBUG _XOPEN_SOURCE 700 _GNU_SOURCE _FORTIFY_SOURCE 2 ABSL_FORCE_ALIGNED_ACCESS BOOST_ENABLE_ASSERT_DEBUG_HANDLER BOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF BOOST_LOG_NO_SHORTHAND_NAMES BOOST_LOG_USE_NATIVE_SYSLOG BOOST_LOG_WITHOUT_THREAD_ATTR BOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS BOOST_SYSTEM_NO_DEPRECATED BOOST_THREAD_USES_DATETIME BOOST_THREAD_VERSION 5' }, bits: 64, debug: false, maxBsonObjectSize: 16777216, storageEngines: ['devnull', 'wiredTiger'], ok: 1, '$clusterTime': { clusterTime: Timestamp({ t: 1744970998, i: 3 }), signature: { hash: Binary.createFromBase64('M00heSbr3iAsV0QJXgPdGT38oh4=', 0), keyId: Long('7482819781188386822') } }, operationTime: Timestamp({ t: 1744970998, i: 3 }) } ``` ```auto [root@percona-backup-mongodb-c44dbcdcf-cmb4r /]# pbm backup --type=logical Starting backup '2025-04-18T10:05:45Z'....Backup '2025-04-18T10:05:45Z' to remote store '/backups/' [root@percona-backup-mongodb-c44dbcdcf-cmb4r /]# pbm backup --type=physical Starting backup '2025-04-18T10:08:52Z'.................................Error: get backup metadata: get: context deadline exceeded ``` ```auto 2025-04-18T10:08:53.000+0000 I got command backup [name: 2025-04-18T10:08:52Z, compression: s2 (level: default)] , opid: 680224b495032062a1d65208 2025-04-18T10:08:53.000+0000 I got epoch {1744970633 5} 2025-04-18T10:08:53.000+0000 I got command backup [name: 2025-04-18T10:08:52Z, compression: s2 (level: default)] , opid: 680224b495032062a1d65208 2025-04-18T10:08:53.000+0000 I got epoch {1744970633 5} 2025-04-18T10:08:53.085898089Z 2025-04-18T10:08:53.000+0000 E [backup/2025-04-18T10:08:52Z] node check: full physical backup works since Percona Server for MongoDB 4.2.15, 4.4.6 2025-04-18T10:08:53.000+0000 I [backup/2025-04-18T10:08:52Z] node is not suitable for backup 2025-04-18T10:08:53.000+0000 E [backup/2025-04-18T10:08:52Z] node check: full physical backup works since Percona Server for MongoDB 4.2.15, 4.4.6 2025-04-18T10:08:53.000+0000 I got command backup [name: 2025-04-18T10:08:52Z, compression: s2 (level: default)] , opid: 680224b495032062a1d65208 2025-04-18T10:08:53.000+0000 D [backup/2025-04-18T10:08:52Z] init backup meta 2025-04-18T10:08:53.000+0000 I got epoch {1744970633 5} 2025-04-18T10:08:53.000+0000 E [backup/2025-04-18T10:08:52Z] node check: full physical backup works since Percona Server for MongoDB 4.2.15, 4.4.6 2025-04-18T10:08:53.000+0000 D [backup/2025-04-18T10:08:52Z] nomination list for rs0: [] 2025-04-18T10:09:08.000+0000 D [backup/2025-04-18T10:08:52Z] nomination timeout 2025-04-18T10:09:08.000+0000 D [backup/2025-04-18T10:08:52Z] skip after nomination, probably started by another node ``` ---
**Author:** ![liking](https://sea1.discourse-cdn.com/flex019/user_avatar/forums.percona.com/liking/32/5574_2.png) [@liking](https://forums.percona.com/u/liking)\ **Post date:** [November 7, 2025, 9:22am UTC](https://forums.percona.com/t/pbm-agent-on-docker-running-into-storage-is-not-initialized/37534/12 "2025-11-07T09:22:12Z")
I met the same problem. It seems pbm can’t make a physical backup on native mongodb cluster. My cluster version is 7.0.1. ---
**Author:** ![Ivan\_Groenewold](https://sea1.discourse-cdn.com/flex019/user_avatar/forums.percona.com/ivan_groenewold/32/6299_2.png) [@Ivan\_Groenewold](https://forums.percona.com/u/Ivan_Groenewold)\ **Post date:** [November 7, 2025, 11:05am UTC](https://forums.percona.com/t/pbm-agent-on-docker-running-into-storage-is-not-initialized/37534/13 "2025-11-07T11:05:35Z")
Hi, please open a new thread with details about your case ---
**Author:** ![Ivan\_Groenewold](https://sea1.discourse-cdn.com/flex019/user_avatar/forums.percona.com/ivan_groenewold/32/6299_2.png) [@Ivan\_Groenewold](https://forums.percona.com/u/Ivan_Groenewold)\ **Post date:** [November 7, 2025, 11:05am UTC](https://forums.percona.com/t/pbm-agent-on-docker-running-into-storage-is-not-initialized/37534/14 "2025-11-07T11:05:39Z")